Re: [Freesurfer] Question on lateral ventricle segmentation

[Douglas N. Greve]

No, there is not an easy way to break it up that way. If you know some 
programming, you could merge all 3 into one seg, then compute the PCA of 
the coordinates, then divide it up along the largest direction


On 9/9/2024 1:54 AM, Necati Emre Şahin wrote:


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Dear FreeSurfer Developers,
I hope this message finds you well.

I am currently working with FreeSurfer 7.4.1 and I have encountered a situation that  I would like 
your guidance on. Specifically, I have noticed that FreeSurfer  outputs the lateral ventricle in 
two parts for sides, namely "Left-Lateral-Ventricle" and  "Left-Inf-Lat-Vent" 
for left. However, from an anatomical perspective, I am interested  in obtaining the results for 
the four parts of the lateral ventricle  separately: the anterior horn, central part, posterior 
horn, and inferior horn.

I understand that the "Left-Inf-Lat-Vent" might correspond to the inferior  
horn. Is FreeSurfer capable of providing the segmentation for the lateral  ventricle in 
these specific sub-regions? If not, could you recommend any method  or workaround that 
would allow me to obtain these detailed segmentations?

Additionally, if it is not possible to directly obtain these sub-regional  
volumes, is there a way to derive the ventricle volumes within each lobe (e.g., 
 frontal, parietal, occipital, temporal) using FreeSurfer or any other tool?

Your assistance in this matter would be greatly appreciated. Thank you for your 
time and support.

Best regards,

Necati Emre Sahin.

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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

Does it run with the --cpu flag? That will run it with the cpu and thus 
isolate your problem to the gpu/cuda


On 9/9/2024 10:31 PM, Matthew Lynch wrote:


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I run this command:

mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o 
/mnt/p/test


and it fails with the following (partial) error message:

Node: 'model_3/unet_conv_downarm_0_0/Conv3D'
DNN library is not found.

which I assume means it cannot access the appropriate the CuDNN library.

I have installed

GPU: nvidia geforce RTX 3050 Ti (4Gb)
WSL2
Linux kernel: 5.15.153.1-microsoft-standard-WSL2 (after recent wsl 
--update)

CUDA Version 12.6
Windows Nvidia Driver version 560.94
CuDNN Version 9.4.0 installed in WSL, with libraries located 
in /lib/x86_64-linux-gnu


However, freesurfer's tensorflow seems to point to its own cudnn 
libraries in:

/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/nvidia/cudnn/lib

including

libcudnn.so.8

which I assume is CuDNN version 8, and may not be compatible with CUDA 
12.6?


Is there a way I can get freesurfer's script to use the CuDNN 9.4.0 
that are installed globally on the WSL system?  Any other suggestions 
on what might be causing this error and how to fix it?



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Re: [Freesurfer] Error in dt_recon

[Douglas N. Greve]

The argument to the --s flag should be the name of the subject as was 
specified when you ran recon-all, eg

recon-all -i t1_SPGR.nii  -s subjectname -all
Then use dt_rcon -s subjectname ...

On 9/12/2024 7:45 AM, Ramesh Babu wrote:


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Dear All,

I am new to dti analysis. I am trying analysis in a single subject. I 
set the environment as mentioned below.
export DTI_DATA=export 
DTI_DATA=/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis

export SUBJECTS_DIR=$DTI_DATA/subjects/t1_data/

In the last step, I received this error.
dt_recon --i dti_data.nii --b bvals.txt bvecs.txt --s 
$SUBJECTS_DIR/t1_SPGR.nii --o dtioutput2
error: 
mghRead(/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis/subjects/t1_data//t1_SPGR.nii/mri/brainmask.mgz, 
-1): could not open file


How to get this brain mask? Should it be from subject T1 image or bo map?
I attached the full error report as a text file.
I kindly request you to provide me with a solution.

Thanks in advance
Ramesh

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Re: [Freesurfer] Longitudinal base processing error

[Douglas N. Greve]

that could certainly be a problem. Is it really just a single value 
throughout the brain? If so, that is the problem. On the other hand, it 
could be that the freeview intensity limits are not set well, so try 
playing with those. You can also click on voxels in the brain and look 
at the values in the panel.


On 8/23/2024 11:52 AM, Nelson, Eric (Campus) wrote:


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Hello all,

I am using the longitudinal pipeline and keep getting the following 
error when generating the base for one of our subjects. I have 3 
timepoints I am including. I have checked the nu.mgz and orig.mgz 
files for both the base and each time point. Everything looks fine 
with the exception of the nu.mgz for timepoint 1 (which is a solid 
white and looks like a mask). Could this be the problem? I have re-run 
recon-all for that cross sectional subject, but the image remains the 
same. Attached the full recon-all.log from the base output.


3d normalization pass 1 of 2

error: MRInormFindControlPoints: could not find enough control points

error: MRInormFindControlPoints failed

@#@FSTIME  2024:08:16:18:05:30 mri_normalize N 10 e 10.45 S 0.04 U 
10.40 P 99% M 434992 F 0 R 10859 W 0 c 4 w 11 I 0 O 0 L 1.14 0.90 0.57


@#@FSLOADPOST 2024:08:16:18:05:40 mri_normalize N 10 1.19 0.92 0.58

Linux c0235 3.10.0-1160.24.1.el7.x86_64 #1 SMP Thu Mar 25 21:21:56 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux


Best,

*Eric Nelson, Ph.D. | Postdoctoral Fellow*

Department of Psychiatry and Behavioral Neurobiology

School of Medicine

UAB | The University of Alabama at Birmingham


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Re: [Freesurfer] Recon-all -all for many MRI sequences?

[Douglas N. Greve]

you have to pass it the file(s) you want to analyze. If you have a bunch 
of dicoms, and your T1 is just one of many, you have to figure out one 
of the files that corresponds to the T1. Or you can use dcmunpack, eg,

dcmunpack -src /path/to/your/dicoms -targ outputfolder -auto-runseq mgz
That command will find all the series and convert each one to an mgz 
file. Hopefully, it will be obvious after that which one is the T1


On 8/22/2024 10:48 PM, 김유진 wrote:


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Hello,


I have many dicom files with many MRI sequences from one person.

(T1, T2, FLAIR, DWI, ...)

I didn't divided the folders according to the sequences-they are 
all in one folder.


Then does the program sort T1 image automatically and make results 
when I do 'recon-all -all -i  -s '?


Or does the program use all the files?

And I wonder that Freesurfer offers code for sorting the files based 
on sequences.



Thank you in advance!


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Re: [Freesurfer] petsurfer questions - No PVC stats file in the similar format as gtm.stats.dat

[Douglas N. Greve]

looks like it is only different in the first or second decimal place, is 
that right? If so, then it is acceptable.


On 8/22/2024 4:11 PM, Sneha Pandya wrote:


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Dear team,

A] I am running mri_gtmpvc on our data and need to extract stats data 
that is in the similar format as gtm.stats.dat file from non-pvc 
corrected PET data, in the sense getting mean regional uptake from 
non-pvc PET data alongside region names, volumes, var, etc information 
using ROIs from gtmseg.


mri_gtmpvc command (turned off PVC):

mri_gtmpvc --i PET.nii.gz --reg PET_to_nu.reg.lta --seg ${ 
FreeSurferDir }/mri/gtmseg.mgz --default-seg-merge --auto-mask ${FWHM} 
.01 --psf 0 --no-tfe --no-rescale --save-input --o nopvcoutput


I tried this with following approaches as suggested in the forum:

1] mri_convert nopvc.nii.gz --ascii nopvc_1.stats.dat

2] mri_segstats --i input.nii.gz --seg aux/seg.nii.gz --ctab 
aux/seg.ctab --excludeid 0 --sum nopvc_2.stats.dat


On comparing mean uptake between nopvc_1.stats.dat and 
nopvc_2.stats.dat, I see that values are similar but not same. Is this 
expected?


Head of nopvc_1.stats.dat:

54832.960938

65543.554688

59080.023438

75662.140625

47840.519531

61120.222656

66590.773438

69356.742188

58847.007812

65715.578125

Head of nopvc_2.stats.dat:

Index



SegId



NVoxels



Volume_mm3



StructName



Mean



StdDev



Min



Max



Range

1



2



106905



223886.7



Left-Cerebral-White-Matter



54832.95



8839.049



15160.92



96317.77



81156.85

2



7



7723



16174



Left-Cerebellum-White-Matter



65543.57



10289.78



26951.39



90987.36



64035.97

3



8



24806



51950.2



Left-Cerebellum-Cortex



59079.91



14349.17



13388.75



107889.7



94500.95

4



10



3427



7177



Left-Thalamus



75662.06



13054.39



33599.36



105854.3



72254.89

5



11



1813



3796.9



Left-Caudate



47840.52



10624.56



19515.38



88224.69



68709.31

6



12



2280



4774.9



Left-Putamen



61120.21



8453.317



43591.13



83701.97



40110.84

7



13



976



2044



Left-Pallidum



66590.77



5816.431



50056.58



83431.62



33375.04

8



16



6686



14002.2



Brain-Stem



69356.77



16951.96



20199.62



115301.7



95102.11

B] Also, when we turn off PVC with “--psf 0 --no-tfe” flags, SGTM is 
still performed right whose regional data is saved in gtm.stats.dat 
file? If we perform RBV PVC does it in addition affect in anyway SGTM 
outputs (i.e gtm.stats.dat)?


C] Is there a way to erode only reference region in the mri_gtmpvc 
command both when PVC is performed (SGTM or RBV) and with no PVC? If 
not, is there a way to do so after running mri_gtmpvc to rescale 
PVC’ed and non-PVC’ed uptake with eroded cerebellum derived from 
gtmseg? I have extracted eroded GM cerebellum from gtmseg using 
mri_binarize and then planning to use that eroded GM cerebellum mask 
to rescale PVC’ed/non-PVC’ed regional uptake, not sure if it is the 
right approach.


mri_binarize command:

mri_binarize --i ${FreeSurferDir}/mri/gtmseg.mgz --o 
CerebellumGrayMatterMaskEroded_gtmseg.mgz --match 8 47 --erode 2


Thank you,

Sneha


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Re: [Freesurfer] PetSurfer: PET SUVR analysis

[Douglas N. Greve]

On 8/13/2024 12:38 AM, WONG Wan Wa wrote:


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Hi FS experts,

I want to do PET SUVR analysis using PetSurfer. When determining the 
FWHM of the PSF of the scanner, is it the same value for Siemens 
(Biograph40_mCT vs. Biograph128_mCT) or (Biograph64_Vision 600 vs. 
Biograph128_Vision 600 Edge)?
I don't know. Usually, there is some literature on a give system about 
what the PSF is.
We also have data collected with GE scanner. Are we able to use the 
ComBat to do harmonization for all calculated SUVR values across 
different sites/scanners with the use of same tracer (e.g. PiB)?

I don't know.


Thanks,
Angel


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Re: [Freesurfer] How to change mri_convert --conform to use another flag while running recon-all

[Douglas N. Greve]

You can add -cubic to the recon-all command line (though you might get 
cubic at other times, but that probably won't hurt)


On 8/19/2024 1:40 PM, Jeiran Choupan wrote:


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Dear Freesurfer support team,

I noticed that the interpolation setting used within the first few 
steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is 
reducing the data quality for data that has a rectangular field of view.


I need to use the `mri_convert` with another flag setting, and I was 
wondering if there’s a way to smoothly do this. This command is used 
twice within the recon-all. And I only need to change the second time 
it is used. The first time is to rename/convert the original file to 
“mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ 
will be converted to “mri/orig.mgz” using “—conform”. I only need to 
change the second time it is used, and I need to use the flag 
“--resample_type cubic “.


Any help is much appreciated


Kind regards,
Jeiran


Jeiran Choupan, PhD, MSCS

Assistant Professor of Research Neurology
Laboratory of Neuro Imaging
USC Stevens Neuroimaging and Informatics Institute
Keck School of Medicine
University of Southern California

2025 Zonal Ave, Los Angeles, CA 90033, USA
(323) 44-BRAIN

image001.pngimage002.png


On Aug 15, 2024, at 11:15 AM, Jeiran Choupan  wrote:

Dear Freesurfer support team,

I noticed that the interpolation setting used within the first few 
steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is 
reducing the data quality for data that has a rectangular field of view.


I need to use the `mri_convert` with another flag setting, and I was 
wondering if there’s a way to smoothly do this. This command is used 
twice within the recon-all. And I only need to change the second time 
it is used. The first time is to rename/convert the original file to 
“mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ 
will be converted to “mri/orig.mgz” using “—conform”. I only need to 
change the second time it is used, and I need to use the flag 
“--resample_type cubic “.


Any help is much appreciated


Kind regards,
Jeiran


Jeiran Choupan, PhD, MSCS

Assistant Professor of Research Neurology
Laboratory of Neuro Imaging
USC Stevens Neuroimaging and Informatics Institute
Keck School of Medicine
University of Southern California

2025 Zonal Ave, Los Angeles, CA 90033, USA
(323) 44-BRAIN






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Re: [Freesurfer] PetSurfer: how to convert nopvc.nii.gz to a format like gtm.stats.dat?

[Douglas N. Greve]

You can run something like
mri_convert nopvc.nii.gz --ascii nopvc.dat
This will give you a text file
To put a bunch together across subject, you can run something like
mri_concat */nopvc.nii.gz --o all.nopvc.nii.gz
Then do the same trick as above.


On 8/20/2024 12:01 AM, WONG Wan Wa wrote:


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Any idea?

*Angel Wong, PhD*
Scientific Officer
Hong Kong Center for Neurodegenerative Diseases (HKCeND)


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of WONG Wan Wa 


*Sent:* Thursday, August 15, 2024 12:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [Freesurfer] PetSurfer: how to convert nopvc.nii.gz to a 
format like gtm.stats.dat?


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Hi experts,

As stated in the subject, how to convert "nopvc.nii.gz" generated by 
"mri_gtmpvc" to a format like "gtm.stats.dat"? Moreover, how to 
consolidate all "gtm.stats.dat"'s PVC uptake values of ROIs from 
different subjects in one spreadsheet? Is there any existing command 
to do that?


Thanks,
Angel


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Re: [Freesurfer] Question: Recon-all Using T1/T2 Mutual Information

[Douglas N. Greve]

I'm not sure what you mean. Usually, one would edit the proper volumes 
in freeview using the protocol described (eg, setting edited voxels to 
certain values). One can implement automatic edits as long as one keeps 
to the protocol.


On 7/30/2024 5:09 PM, Edwards, Vincent wrote:


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Hello Freesurfer team!
We are editing brain scans using T1/T2 mutual information to improve 
the original image. Are the recon-all flags the same with as they 
would be when editing using only the T1 images (i.e., recon-all -cp, 
-pial, -wm), or are there additional flags are needed after editing?


Thank you,

Vincent Edwards

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Re: [Freesurfer] FreeSurfer in fmriprep

[Douglas N. Greve]

The log file says that recon-all finished without error. The command 
(robust register) was not called during recon-all. It must be called by 
fmriprep at some point. I don't understand what they are trying to do. 
It looks like they are registering the FS-conformed anatomical volume 
back to the native space, which would not make sense. Sorry, I'm going 
to have to send you back to the fmriprep folks.


On 7/29/2024 6:00 PM, Tengwen Fan wrote:


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Hi Dr. Greve,

Thanks for your reply! Attached is the recon-all.log file.

Please let me know if more information is needed!  Thanks so much!

Best,
Tengwen



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Monday, July 29, 2024 12:26 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] FreeSurfer in fmriprep


You don't often get email from dgr...@mgh.harvard.edu. Learn why this 
is important <https://aka.ms/LearnAboutSenderIdentification>



please send the recon-all.log file in the scripts folder

On 7/23/2024 2:14 PM, Tengwen Fan wrote:


External Email - Use Caution

Dear FreeSurfer Developers,

I hope this email finds you well!

I am using fMRIprep to do pre-processing. The fMRIprep combines 
methodology from AFNI, ANTs, Freesurfer, FSL, and Mindboggle to do 
preprocessing.


 An error was reported while running the fMRIprep. It seems that it 
was due to the structural data and it was about the registration by 
FreeSurfer. But I am new in the neuroimaging area and not very sure 
about what the error actually is about.


I asked the fmriprep team in neurostars 
(https://neurostars.org/t/fmriprep-error-makeisotropic-warning-not-different-enough-wont-reslice/29839/5 
<https://neurostars.org/t/fmriprep-error-makeisotropic-warning-not-different-enough-wont-reslice/29839/5>) 
and they are also not sure about this and recommended to ask the 
FreeSurfer. Although I am not sure if the FreeSurfer in fmriprep is 
what you also work with, I would like to ask and would really 
appreciate it if you could help explain what error it is. Thanks you 
so much!


The error is attached below. Please let me know if you have any 
questions or if more information is needed!

<https://neurostars.org/t/fmriprep-error-makeisotropic-warning-not-different-enough-wont-reslice/29839/5>

Fmriprep error: makeIsotropic WARNING: not different enough, won't 
reslice! 
<https://neurostars.org/t/fmriprep-error-makeisotropic-warning-not-different-enough-wont-reslice/29839/5>
Summary of what happened: Hi, I am running fmriprep and getting the 
following error. I would really appreciate any help! Please let me 
know if more information should be provided! Thanks so much, tengwen 
Command used (and if a helper script was used, a link to the helper 
script or the command generated): fmriprep-docker 
/Users/Desktop/WL_fMRI/data/BIDS 
/Users/Desktop/WL_fMRI/data/derivatives/fmriprep participant 
--participant-label sub-WLfMRI035 --fs-license-file 
/Users/Desktop/WL_fMRI/licen...

neurostars.org



*The Error is: *

Cmdline:
mri_robust_register --satit --iscale --lta 
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta 
--mov /out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz --dst 
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz

Stdout:
7.3.2
--satit: Will iterate with different SAT to ensure outliers 
below wlimit!

--iscale: Enabling intensity scaling!
--lta: Output transform as 
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta 
.
--mov: Using 
/out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz as movable/source 
volume.
--dst: Using 
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz 
as target volume.
reading source 
'/out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz'...
reading target 
'/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz'...

Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
  Type Source : 0  Type Target : 3  ensure both FLOAT (3)
  Reordering axes in mov to better fit dst... ( -1 -3 2 )
Determinant after swap : 1
  Mov: (0.5, 0.5, 0.5)mm  and dim (512, 512, 512)
  Dst: (0.5, 0.5, 0.5)mm  and dim (360, 512, 512)
  Asserting both images: 0.5mm isotropic
    - reslicing Mov ...
      -- changing data type from 0 to 3 (noscale = 0)...
    -

Re: [Freesurfer] FreeSurfer Question

[Douglas N. Greve]

please send your command line, terminal output, and stats file

On 7/23/2024 3:07 PM, Selena Gangaram wrote:


External Email - Use Caution

Hi,

I hope you are doing well, I subscribed to your mailing list to ask my 
question!


I was wondering if you knew the reason as to why my extraction code in 
FreeSurfer listed regions such as "Whole_hippocampal_body" amongst 
other brain regions twice in my stats files. In my excel stats files I 
have two Whole_hippocampal_body and I wasn't sure what the two 
different values meant. Please help! Thank you!!!


Best,
Selena



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Re: [Freesurfer] FreeSurfer in fmriprep

[Douglas N. Greve]

please send the recon-all.log file in the scripts folder

On 7/23/2024 2:14 PM, Tengwen Fan wrote:


External Email - Use Caution

Dear FreeSurfer Developers,

I hope this email finds you well!

I am using fMRIprep to do pre-processing. The fMRIprep combines 
methodology from AFNI, ANTs, Freesurfer, FSL, and Mindboggle to do 
preprocessing.


 An error was reported while running the fMRIprep. It seems that it 
was due to the structural data and it was about the registration by 
FreeSurfer. But I am new in the neuroimaging area and not very sure 
about what the error actually is about.


I asked the fmriprep team in neurostars 
(https://neurostars.org/t/fmriprep-error-makeisotropic-warning-not-different-enough-wont-reslice/29839/5) 
and they are also not sure about this and recommended to ask the 
FreeSurfer. Although I am not sure if the FreeSurfer in fmriprep is 
what you also work with, I would like to ask and would really 
appreciate it if you could help explain what error it is. Thanks you 
so much!


The error is attached below. Please let me know if you have any 
questions or if more information is needed!



Fmriprep error: makeIsotropic WARNING: not different enough, won't 
reslice! 

Summary of what happened: Hi, I am running fmriprep and getting the 
following error. I would really appreciate any help! Please let me 
know if more information should be provided! Thanks so much, tengwen 
Command used (and if a helper script was used, a link to the helper 
script or the command generated): fmriprep-docker 
/Users/Desktop/WL_fMRI/data/BIDS 
/Users/Desktop/WL_fMRI/data/derivatives/fmriprep participant 
--participant-label sub-WLfMRI035 --fs-license-file 
/Users/Desktop/WL_fMRI/licen...

neurostars.org



*The Error is: *

Cmdline:
mri_robust_register --satit --iscale --lta 
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta 
--mov /out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz --dst 
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz

Stdout:
7.3.2
--satit: Will iterate with different SAT to ensure outliers 
below wlimit!

--iscale: Enabling intensity scaling!
--lta: Output transform as 
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta 
.
--mov: Using 
/out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz as movable/source 
volume.
--dst: Using 
/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz 
as target volume.
reading source 
'/out/sourcedata/freesurfer/sub-WLfMRI033/mri/T1.mgz'...
reading target 
'/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-WLfMRI033_ses-Session1_T1w_noise_corrected.nii.gz'...

Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
  Type Source : 0  Type Target : 3  ensure both FLOAT (3)
  Reordering axes in mov to better fit dst... ( -1 -3 2 )
Determinant after swap : 1
  Mov: (0.5, 0.5, 0.5)mm  and dim (512, 512, 512)
  Dst: (0.5, 0.5, 0.5)mm  and dim (360, 512, 512)
  Asserting both images: 0.5mm isotropic
    - reslicing Mov ...
      -- changing data type from 0 to 3 (noscale = 0)...
    - reslicing Dst ...
      -- Original : (0.5, 0.5, 0.5)mm and (360, 512, 512) voxels.
      -- Resampled: (0.5, 0.5, 0.5)mm and (512, 512, 512) voxels.
      -- Reslicing using cubic bspline
MRItoBSpline degree 3
    - WARNING: trg mri outside_val = 0  but suspected 
background: -0.00687514
              If background is black or darkgray, ignore this. 
If white, pass --whitebgdst

Registration::findSaturation
  - computing centroids
  - computing initial transform
    -- using translation info
  - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
  - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 )
  - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 )
  - Max Resolution used: 3
    -- gpS ( 64 , 64 , 64 )
    -- gpT ( 64 , 64 , 64 )
  - running loop to estimate saturation parameter:
    -- Iteration: 1  trying sat: 16
        min sat: 0 ( -1 ), max sat: 16 ( 0.12101 ), sat diff: 
16, (wlimit=0.16)

    -- Iteration: 2  trying sat: 8
        min sat: 8 ( 0.324589 ), max sat: 16 ( 0.12101 ), sat 
diff: 8, (wlimit=0.16)

    -- Iteration

Re: [Freesurfer] Scalp mask

[Douglas N. Greve]

You can try mri_seghead and/or mideface (which uses mri_seghead)

On 7/16/2024 6:27 AM, Francesco Lomi wrote:


External Email - Use Caution

Hi everybody,
Do you know how to create a scalp mask file with freesurfer?
Thank you in advance
Francesco



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Re: [Freesurfer] Longitudinal analyses using Repeated measures anova

[Douglas N. Greve]

Sorry, there is nothing here (ie, no fsgd file, no images). Did you mean 
to attached?


On 7/10/2024 5:31 AM, Josefine Tingdal Taube Danielsen wrote:


External Email - Use Caution

Hi Freesurfer support,

I'm using Freesurfer version 7.4.1 and Ubuntu 22_x86_64. 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460.



I'm trying to run longitudinal analysis using Repeated Measures Anova 
(https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova).



My study has 2 groups (MM=patient group and HC=healthy controls) and 2 
time points (1 and 2). I am looking at cortical thickness and cortical 
volume.



Here is some information:


We have been using these Contrast files:

# Create 1-vs-2 contrast file

echo "0 0 1" > 1-vs-2.mtx

# Create group-effect contrast file
echo "0 1 0" > group-effect.mtx

# Create interaction contrast file
echo "0 1 -1" > interaction.mtx

# Create mean contrast file
echo "1 0 0" > mean.mtxfree

And then followed this:

Preproc using FSGD

mris_preproc --target fsaverage --hemi lh --meas thickness --out 
lh.thickness.mgh --fsgd rmanova.fsgd



Smooth data

mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.mgh 
--tval lh.thickness.sm05.mgh



Run GLM fit

mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm05.mgh --fsgd 
rmanova.fsgd doss \

  --C 1-vs-2.mtx --C group-effect.mtx --C interaction.mtx --C mean.mtx \
  --surface fsaverage lh

This was our results:
INFO: gd2mtx_method is doss Reading source surface 
/mnt/c/CogimmunStudy/FS/fsaverage/surf/lh.white Number of vertices 
163842 Number of faces 327680 Total area 65417.00 AvgVtxArea 
0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.4.1 cwd 
/mnt/c/CogimmunStudy/FS cmdline mri_glmfit --glmdir lh.rmanova --y 
lh.thickness.sm05.mgh --fsgd rmanova.fsgd doss --C 1-vs-2.mtx --C 
group-effect.mtx --C interaction.mtx --C mean.mtx --surface fsaverage 
lh sysname Linux hostname D56979 machine x86_64 user josdan 
FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y 
/mnt/c/CogimmunStudy/FS/lh.thickness.sm05.mgh logyflag 0 usedti 0 FSGD 
rmanova.fsgd labelmask 
/mnt/c/CogimmunStudy/FS/fsaverage/label/lh.cortex.label maskinv 0 
glmdir lh.rmanova IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 
Creating output directory lh.rmanova Loading y from 
/mnt/c/CogimmunStudy/FS/lh.thickness.sm05.mgh ... done reading. INFO: 
gd2mtx_method is doss Saving design matrix to lh.rmanova/Xg.dat 
Computing normalized matrix Normalized matrix condition is 1 Matrix 
condition is 3.15 Found 149955 points in label. Pruning voxels by thr: 
1.175494e-38 Found 149955 voxels in mask Saving mask to 
lh.rmanova/mask.mgh Reshaping mriglm->mask... search space = 
74612.577841 DOF = 123 Starting fit and test Fit completed in 
0.0220333 minutes Computing spatial AR1 on surface Residual: 
ar1mn=0.986733, ar1std=0.003725, gstd=3.501824, fwhm=8.246166 Writing 
results 1-vs-2 maxvox sig=-2.06583 F=7.13254 at index 102162 0 0 
seed=1720706961 Computing efficiency group-effect maxvox sig=114.013 
F=8295.3 at index 155689 0 0 seed=1720706961 Computing efficiency 
interaction maxvox sig=106.775 F=6297.15 at index 64378 0 0 
seed=1720706961 Computing efficiency mean maxvox sig=133.337 F=17231.6 
at index 155689 0 0 seed=1720706961 Computing efficiency mri_glmfit done


Now our questions:

1.
Have we been using the right contrasts?
2.
Do the results look realistic?
3.
Is it possible to have some more information about results (e.g.
summary, areas being significant, visualization, sig.mgh,
t-values, p-values not i -log10)?


Thank you!

Best,
Josefine Danielsen



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Re: [Freesurfer] Negative voxel ranges

[Douglas N. Greve]

in FS, all the voxel indices are >= 0
I don't know what the numbers mean you put below

On 7/15/2024 6:35 AM, ERNEST KISSI wrote:


External Email - Use Caution

Dear fresurfer team,

Please I want to extract the intensity of a voxel  48, -56, -34. But 
my voxel ranges of my image does not include negative values. Is there 
a way to make the ranges cover these values.


Thanks 👍.

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 .
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Re: [Freesurfer] Very large segmentation errors with recon-all

[Douglas N. Greve]

sorry, nothing attached

On 7/15/2024 4:04 AM, Tornabene, Danilo wrote:


External Email - Use Caution

Hi, and thank you for your answer.

Subject 001 does, indeed, have a misalignment as well, and I don't 
know why ( I checked the files are from the same subject - I can't 
give you a freeview command as I'm using a different software to view 
the results). Subject 017 (also attached) as well as most/all others, 
however, have good alignment but very poor segmentation.
I attached the misaligned picture as well because I thought it could 
give some hint on the problem that occurred.



Best,
Danilo

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Sunday, July 14, 2024 4:56:22 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Very large segmentation errors with recon-all
what you are showing there is not a segmentation error but a severe 
misalignment. What is your freeview command line? Are you sure that 
the anatomicals and the surfaces are from the same subject?


On 7/10/2024 4:59 AM, Tornabene, Danilo wrote:


External Email - Use Caution

Dear FreeSurfer developers,

I've encountered very large, systematic errors in segmentation 
running recon-all on a MRI dataset of 76 subjects. In the screenshot 
attached, you can see how the white surface (shown in the right 
hemisphere) includes most of the cortex as well, while the pial 
surface (in the left hemisphere) extends into the CSF and often 
reaches the skull. In some of the subjects there is also a clear 
misalignment with the T1 images.


I don't have a long experience with FreeSurfer, but my supervisor 
Prof. Cole tells me he has processed thousands of scans and never 
seen this kind of errors so we thought of reaching out to you for 
some help or explanation. The only thing we noticed is that this 
error happens on scans with a higher-than-usual resolution (voxels 
are 0.8x0.8x0.8 mm), could this be causing the problem?


I have simply ran recon-all withouth any additional option or 
argument other than the input files and IDs and the output directory.


Please find the shell log outputs for two sample subjects. The 
recon-all pipeline was completed with no hard errors, and the Euler 
numbers were mostly 2 with some 1.


Best,
Danilo Tornabene

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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>



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Re: [Freesurfer] Maps from fsLR system (32, 492 vertices) to fsaverage5

[Douglas N. Greve]

You'll have to create curvature files, inflate the surface to a sphere, 
then run mris_register

On 7/10/2024 10:10 AM, Stefano Delli Pizzi wrote:
>  External Email - Use Caution
>
> Dear,
>
> We are using the Magicc Maps (https://github.com/kwagstyl/MAGICC). The maps 
> are in fsLR system (32,492 vertices). How can we register them in fsaverage5?
> Thanks
> Best regards
> Stefano
>
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The information in this e-mail is intended only for the person to whom it is 
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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] Very large segmentation errors with recon-all

[Douglas N. Greve]

what you are showing there is not a segmentation error but a severe 
misalignment. What is your freeview command line? Are you sure that the 
anatomicals and the surfaces are from the same subject?


On 7/10/2024 4:59 AM, Tornabene, Danilo wrote:


External Email - Use Caution

Dear FreeSurfer developers,

I've encountered very large, systematic errors in segmentation running 
recon-all on a MRI dataset of 76 subjects. In the screenshot attached, 
you can see how the white surface (shown in the right hemisphere) 
includes most of the cortex as well, while the pial surface (in the 
left hemisphere) extends into the CSF and often reaches the skull. In 
some of the subjects there is also a clear misalignment with the T1 
images.


I don't have a long experience with FreeSurfer, but my supervisor 
Prof. Cole tells me he has processed thousands of scans and never seen 
this kind of errors so we thought of reaching out to you for some help 
or explanation. The only thing we noticed is that this error happens 
on scans with a higher-than-usual resolution (voxels are 0.8x0.8x0.8 
mm), could this be causing the problem?


I have simply ran recon-all withouth any additional option or argument 
other than the input files and IDs and the output directory.


Please find the shell log outputs for two sample subjects. The 
recon-all pipeline was completed with no hard errors, and the Euler 
numbers were mostly 2 with some 1.


Best,
Danilo Tornabene

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Re: [Freesurfer] Functional connectivity: sig.nii.gz values seem off

[Douglas N. Greve]

Have you looked at the individual subjects? This will sometimes happen 
when there are strong global signals as the global signal (by 
definition) gets into the regressor and is everywhere, so you end up 
with these large swaths of positive activation. You're already doing the 
things I would suggest. You can try doing more of it (eg, increase the 
number of components or the number of polynomials). You can  also try 
something like the ithsmus cingulate to generate a default mode map to 
see if that looks typical.


On 7/9/2024 3:56 AM, Doll, Laura wrote:


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Hi,

I ran a functional connectivity analysis according to the walkthrough 
in the Freesurfer Wiki.
After the group analysis (with mri_glmfit using ces and cesvar), I 
plotted the results (sig.nii.gz of the GLM) with freeview, but the 
distribution seems off. I'll attach a screenshot, but in case someone 
cannot access it: There are only few negative data points, the 
majority seems to be in two (!) approx. gaussian distributions 
centered at ~5 (the smaller one) and ~8, so most points have values 
between 5 and 10. Running an FDR correction suggested that the 
threshold should be 1.3


Because the seems highly unlikely, I search the mailing list archive 
and found out about the bug in the functional connectivity analysis.
Therefore, I repeated the group analysis with the pcc instead of the 
ces, but that didn't really change anything.
Side note/question here: There is no variance corresponding to cesvar 
I could use in that case, right?


Any suggestions on what could've gone wrong?

Here are the exact steps I used:

# Create nuisance variables for white matter:
fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config
fcseed-sess -sf Part3HR -cfg wm.config
# Create nuisance variables for ventricles + CSF:
fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config
fcseed-sess -sf Part3HR -cfg vcsf.config

# Auditory cortex
##
# configure parameters
fcseed-config -roi AC-rh -fcname AC-rh.dat -fsd bold -mean -cfg 
AC-rh.config


# create FC seeds
fcseed-sess -sf Part3HR -cfg AC-rh.config

# FC analysis
mkanalysis-sess -analysis fc.AC.surf.rh -surface fsaverage rh -fwhm 5 
-notask -taskreg AC-rh.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 
 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run


selxavg3-sess -sf Part3HR -a fc.AC.surf.rh

isxconcat-sess -sf Part3HR -analysis fc.AC.surf.rh -o AverageFC_AC 
-all-contrasts -map pcc


mri_glmfit --y ./AverageFC_AC/fc.AC.surf.rh/AC-rh/pcc.nii.gz \
    --osgm \
    --surface fsaverage rh \
    --glmdir ./AverageFC_AC/fc.AC.surf.rh/GLM_AC-rh \
    --save-eres \
    --nii.gz


I'd appreciate any input. Thanks in advance!

Best regards,
Laura

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Re: [Freesurfer] Doing math on mgz file

[Douglas N. Greve]

you can also use fscalc, which is a frontend for mris_calc

On 7/9/2024 3:14 PM, Aaron Tanenbaum wrote:


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Perfect thank you

On Tue, Jul 9, 2024 at 1:30 PM Huang, Yujing 
 wrote:


Is this what you are looking for?

https://surfer.nmr.mgh.harvard.edu/pub/docs/wiki/mris_calc.help.xml.html

*From:*freesurfer-boun...@nmr.mgh.harvard.edu
 *On Behalf Of *Aaron
Tanenbaum
*Sent:* Tuesday, July 9, 2024 2:07 PM
*To:* Freesurfer 
*Subject:* [Freesurfer] Doing math on mgz file

*External Email - Use Caution *

Is there an equivalent to fslmaths in freesurfer?

Thank you

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Re: [Freesurfer] Licence for using Freesurfer-generated images in a book?

[Douglas N. Greve]

I think you can use any picture you want without permission.

On 7/8/2024 7:14 AM, ALARIO Francois wrote:


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Hello

I am considering using freesurfer-generated images not in a scientific 
paper but in a popular science book (commercial).


What is the preferred course of action, license-wise, for this 
specific purpose?


Can I include images of fsaverage with Desikan atlas parcellations, or 
should I avoid using fsaverage and use instead images I have acquired?


The general license is worded in terms of “Software”, but said figures 
would not appear to laypeople to be “Software”


May I skip the words

"All or portions of this licensed product (such portions are the 
"Software") have been obtained under license from The General Hospital 
Corporation and are subject to the following terms and conditions:"


and more plainly acknowledge that the images were created with 
Freesurfer by citing


''Cortical reconstruction and volumetric segmentation was performed 
with the Freesurfer image analysis suite, which is documented and 
freely available for download online 
()'',


along with one of the papers (which one)?

The book is in French the recommended option would be translated to 
French.


Any advice would be appreciated.

Kind regards

Xavier

--

Xavier ALARIO

+ 33 4 13 55 09 72

https://cv.hal.science/f-xavier-alario

https://crpn.univ-amu.fr/fr/annuaire/alario-xavier


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Re: [Freesurfer] mri_gtmpvc RBV - cannot find file from a custom subject directory

[Douglas N. Greve]

That is the way I would have suggested. Does it run to completion when 
you use the softlink? Reorganizing the folder structure it likely to 
break a lot of things.


On 7/11/2024 10:02 AM, Sneha Pandya wrote:


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Dear team,

I am running mri_gtmpvc using RBV correction, however when I do so I 
get an error message saying it cannot find 
$SUBJECTS_DIR/$subject_id/mri/orig.mgz needed for RBV.


Our Freesurfer outputs are nested as 
$subject_id/MPRAGE/Freesurfer/mri/orig.mgz. I tried mri_gtmpvc with 
“--sd” flag as well, still same error as when I set “--sd 
$subject_id/MPRAGE/Freesurfer” it tries to find the file as 
$subject_id/MPRAGE/Freesurfer/$subject_id/mri/orig.mgz. One way I can 
avoid doing this is by creating a soft link with the expected path, 
however if there is a better way to do so that would be great.


Thank you,

Sneha


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Re: [Freesurfer] Robustness of Segmentation and Parcellation to Lesions

[Douglas N. Greve]

On 7/3/2024 7:19 PM, Hickman, Leonard B. MD wrote:


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Hello all,

I am using FreeSurfer to measure specific cortical parcellations and 
subcortical segmentations in a medium-sized dataset (over 150 scans). 
About a fifth of the scans include cortical lesions (ischemic stroke, 
hemorrhagic stroke, focal traumatic injuries, neoplasm) that visibly 
disrupt recon-all's white matter surface and the pial surface locally 
at the lesion.


Assuming there is no midline shift, does the recon-all processing 
stream perform segmentations and parcellations in each hemisphere 
independently? Or, could a unilateral lesion impact 
segmentation/parcellation on the contralateral side?
The segmentation is done on each hemi separately. A lesion on one side 
should not affect the contralateral side.


For segmentation/parcellation measurements on the side ipsilateral to 
a lesion, how robust are recon-all's measurements in non-lesioned 
regions? For instance, are hippocampal volume measurements impacted by 
a cortical lesion in the frontal convexity? Or a lesion in a lateral 
temporal gyrus? Are there any general guides on how close a lesion can 
be to a ROI before automated measurements are invalid?
I think a lesion would have to be adjacent to a given structure to 
affect its segmentation, at least between cortical lesions and 
subcortical structures as your describe. For cortical-cortical, there 
could be some effect as the surface placement might be affected. If the 
curvature is affected, then it could change the registration to fsaverage.


Thank you much in advance,
Brian
--
L. Brian Hickman, MD, MSc



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Re: [Freesurfer] data in folder 'stats'

[Douglas N. Greve]

It is not normalized. these are volumes, surface ares, and thicknesses 
of various regions. I'm not sure what common space corrections you could 
do. You can correct for eTIV


On 7/3/2024 1:11 PM, PATRICIO FELIPE RIQUELME wrote:


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Hi everyone.
I just began to use freesurfer, and I wanna know if the data in folder 
'stats', after recon-all processing, is normalized in a common space 
or if I need to correct it in an additional step.

Thank you

Patricio Riquelme

Departamento de Tecnología Médica
Facultad de Medicina
Universidad de Chile

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Re: [Freesurfer] Scanner and Freesurfer-version differences

[Douglas N. Greve]

On 7/1/2024 1:05 AM, Bronwyn Overs wrote:


External Email - Use Caution

Hi Freesurfer Mailing List,

I work on a large bipolar disorder imaging study that has been running 
for over 10 years. We previously acquired 2 sMRI time-points (pre 
2013, /n/~500, /n/~250 at each time-point) on a single Philips 3T 
scanner and these images were processed with Freesurfer version 5.3. 
We have just now acquired a third imaging time-point that was 
completed on a different scanner (Siemans, /n/~120) using a different 
acquisition protocal. So I have three questions for the mailing list, 
that I'm hoping will inform the design of our analysis protocol:


 1. Are there specific considerations for processing structural MRIs
that have been acquired on different scanners and with different
acquisition protocols?

No, we don't have anything special for this. Our experience is that the 
cortical results tend to be much less dependent upon the actual 
acquisition parameters and scanners.


 1. Reprocessing all time 1 and time 2 images with a newer version of
Freesurfer is a huge undertaking (for both processing time and
personnel time required to review and edit). However, is there a
reason why a newer version of Freesurfer should be used (e.g.
publication considerations, more consistent output) as opposed to
processing time 3 with v5.3?

I think you are ok to continue to use 5.3. Reviewers are pretty lenient 
about these kind of thing. Given the incremental longitudinal nature of 
the project, you can just switch and rerun everything.


 1. I know there are differences in the output across different
versions of Freesurfer. However, do different system set ups (e.g.
linux, mac, as well as operating systems) have an impact on the
output, even if the same version of Freesurfer is used?

You can get differences that are very small but systematic. If it is 
something you are worried about, treat the OS as another variable in the 
sense that you randomize the OS across your variables of interest (ie, 
don't have all your patients be from one OS and all your controls be 
from another). You could test the effect of OS; if it is not 
significant, you can remove it from the analysis.


Kind regards,


Bronwyn Overs

Research Assistant


Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1725


neura.edu.au 

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Re: [Freesurfer] Inquiry about alpha inflation in multiple comparison

[Douglas N. Greve]

Have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm

On 6/28/2024 9:48 AM, Emma Harper wrote:


External Email - Use Caution

Dear Freesufer teams,

Does anyone have any recommendations to correct for alpha inflation 
when doing the multiple comparisons in freesurfer? We are trying to 
avoid using the Bonferroni Correction so any recommendations for ways 
beside that would be greatly appreciated.


Thanks,
Emma Harper

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Re: [Freesurfer] FreeSurfer atlases

[Douglas N. Greve]

Try looking at it in freeview first. Some of the regions may be small, 
so you may have to hunt to get them. FYI you can specify nii as the 
output of mri_binarize


On 6/28/2024 5:30 AM, Savoia, Alice (Stud. FPN) wrote:


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Thank you for the reply,
I need to create a mask of each segmented subfield (segmented with 
freesufer) and then I need to use the obtained mask in FSL to do a 
DTI. However, I am not sure about the pipeline I have to follow to do 
so. So far I have been following this one:


  * mri_label2vol --seg <> --temp rawavg.mgz --regheader <> --o "".mgz
  * mri_binarize --i --o --match "17"


  * mri_convert --in_type mgz --out_type nii


  * flirt -in -out -init  -applyxfm


  * fslmaths -bin


But when I try to open the mask in FSL I cannot visualize them. Does 
anyone have suggestions?

Thanks,
Alice

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, June 27, 2024 12:36 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] FreeSurfer atlases
I'm not sure what you mean. We don't have an image of the subfields 
in, eg, mni space. Usually, you just run the subfield seg on the data 
that you want subfields for


On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote:


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Hello,
I am looking for a freesufer standard atlas for hippocampal subfields 
(to be used for a DTI pipeline in FSL) but I cannot find it in 
fsaversage/label.

Does anyone have any suggestion?
Thank for the help,
Alice

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Re: [Freesurfer] Error saying cannot find my file for recon-all

[Douglas N. Greve]

It can't find the file struct.nii. You have to give it the full path to 
the file. It looks like $Users is not set to anything (blank)


On 6/28/2024 12:03 AM, Lydia Luck wrote:


External Email - Use Caution

Hello-

I am trying to do recon-all on my brain MRI and I’ve rewritten it so 
many times I have absolutely no clue what is going wrong. Ultimately, 
the main error message I’m getting is that my file is not found. I’ve 
tried typing out the complete path, made multiple different folders, 
renamed the file and the folders, changed the file type, changed the 
location of the folder, exited terminal and tried again, switched to 
the other user on the computer (got the same error) even restarted my 
computer, etc. Kind of at a loss at this point. I am using a Mac with 
an M1 chip and the 7.4.1 version


This is my current line of commands:

export FREESURFER_HOME=/Applications/freesurfer/7.4.1

source $FREESURFER_HOME/SetUpFreeSurfer.sh

export FS_LICENSE=/opt/freesurfer/license.txt

export SUBJECTS_DIR=$Users/lydialuck/3DBRAIN

recon-all -s lydiasbrain -i $Users/lydialuck/3DBRAIN/struct.nii.gz 
-parallel -all



And then getting this back:

ERROR: cannot find /lydialuck/3DBRAIN/struct.nii.gz

Darwin Blazes-MBP.lan 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 
21:44:06 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T8103 arm64



recon-all -s lydiasbrain exited with ERRORS at Thu Jun 27 01:13:56 EDT 
2024



If you could help me figure this out that would be great; I’ve 
probably spent well over 6 hours now trying different things.



Thanks so much,

Lydia


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Re: [Freesurfer] 回复: The file absence problem of the recon-all -all output

[Douglas N. Greve]

Use orig.mgz

On 6/27/2024 9:47 PM, Quanjiang Liu wrote:


External Email - Use Caution

  Sorry to bother you again. I want to know that the standard input to 
get the standard lh.seghead and rh.seghead. Is it the T1.mgz or the 
brain.mgz in the mri folder which is one of the output files of 
recon-all -all command.

Best,


*发件人:* freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N. Greve 


*发送时间:* 2024年6月27日 6:35
*收件人:* freesurfer@nmr.mgh.harvard.edu 
*主题:* Re: [Freesurfer] The file absence problem of the recon-all -all 
output



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that has to be created with a separate process (mri_seghead)

On 6/26/2024 2:11 PM, Quanjiang Liu wrote:


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  Hi, I ran the recon-all -all command successfully. But the 
lh.seghead and rh.seghead didn't appear in my output folder. The 
attachment is the process record. Can you help to solve it?

  Sorry to bother.
Best

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Re: [Freesurfer] FreeSurfer atlases

[Douglas N. Greve]

I'm not sure what you mean. We don't have an image of the subfields in, 
eg, mni space. Usually, you just run the subfield seg on the data that 
you want subfields for


On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote:


External Email - Use Caution

Hello,
I am looking for a freesufer standard atlas for hippocampal subfields 
(to be used for a DTI pipeline in FSL) but I cannot find it in 
fsaversage/label.

Does anyone have any suggestion?
Thank for the help,
Alice

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Re: [Freesurfer] The file absence problem of the recon-all -all output

[Douglas N. Greve]

that has to be created with a separate process (mri_seghead)

On 6/26/2024 2:11 PM, Quanjiang Liu wrote:


External Email - Use Caution

  Hi, I ran the recon-all -all command successfully. But the 
lh.seghead and rh.seghead didn't appear in my output folder. The 
attachment is the process record. Can you help to solve it?

  Sorry to bother.
Best

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Re: [Freesurfer] MRI watershed error

[Douglas N. Greve]

not sure, it might work

On 6/26/2024 2:21 PM, Gaurav Ambwani wrote:


External Email - Use Caution

Dear Freesurfer team,

In short I just wanted to know if it would be possible for me to put a 
skull stripped MRI into freesurfer for recon-all?


Thank you,
Best Wishes,
Gaurav Ambwani.

*From:* Gaurav Ambwani 
*Sent:* Wednesday, June 26, 2024 2:12 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] MRI watershed error
Dear Freesurfer team,

The issue with that is that on fsl I would need to skull strip the 
image that I want to input for the registration. The reference image 
doesn't have to be skull stripped, but the input image has to be skull 
stripped.


When I take the skull stripped image as my reference image and input 
the T1 MNI image, the registration isn't successful, i.e. the image 
seems warped.


Thank you,
Best Wishes,
Gaurav Ambwani.

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Tuesday, June 25, 2024 9:51 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] MRI watershed error
you can compute the registration with the skull-stripped image, and 
then apply the registration to the whole head image


On 6/25/2024 12:31 PM, Gaurav Ambwani wrote:


External Email - Use Caution

Dear Freesurfer team,

I can't put the whole head into FSL for registration, I have to put 
the skull stripped version into FSL. I have to put in the skull 
stripped head because the MNI_freesurfer_T1.nii.gz  is registered to 
the stroke patient's T1 weighted image.


Using the I want the aseg, aparc, etc. files to be derived from the 
MNI_freesurfer_T1.nii.gz image. And for some reason it isn't working. 
I hope that this clarifies what I was trying to do.


Thank you,
Best Wishes,
Gaurav Ambwani.

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas 
N. Greve  <mailto:dgr...@mgh.harvard.edu>

*Sent:* Monday, June 24, 2024 9:50 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] MRI watershed error
Sorry, I'm not sure what the problem is that you are describing. I 
see from the recon-all file that

MNI_freesurfer_T1.nii.gz is your input. What is that? Is that after skull 
stripping? Why not just give it the full head?
On 6/20/2024 3:52 PM, Gaurav Ambwani wrote:


External Email - Use Caution

Dear Freesurfer developers,

I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain 
extraction tool in 3D slicer, and then I registered it in fsl to a 
skull stripped version of a T1 weighted image of a Stroke patient 
(which I got from Openneuro).


The purpose of doing this is to, get the aseg.mgz file and overlay 
that onto the MRI of the stroke patient.


Previously I have taken the T1 1mm MNI image and received an 
aseg.mgz file which I have overlayed onto my MNI registered T1 
weighted stroke MRI and that worked perfectly. However, This time I 
have taken the T1 1mm MNI image registered that to my stroke T1 MRI, 
and the registered image hasn't gone through freesurfer.


I have attached the recon-all.log file in this email.

Freesurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1 
SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Distributor ID: Ubuntu
Description:    Ubuntu 22.04.4 LTS
Release:        22.04
Codename:       jammy

I am using a WSL in windows 11 (64 bit)

Thank you,
Best Wishes,
Gaurav Ambwani.

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Re: [Freesurfer] MRI watershed error

[Douglas N. Greve]

you can compute the registration with the skull-stripped image, and then 
apply the registration to the whole head image


On 6/25/2024 12:31 PM, Gaurav Ambwani wrote:


External Email - Use Caution

Dear Freesurfer team,

I can't put the whole head into FSL for registration, I have to put 
the skull stripped version into FSL. I have to put in the skull 
stripped head because the MNI_freesurfer_T1.nii.gz  is registered to 
the stroke patient's T1 weighted image.


Using the I want the aseg, aparc, etc. files to be derived from the 
MNI_freesurfer_T1.nii.gz image. And for some reason it isn't working. 
I hope that this clarifies what I was trying to do.


Thank you,
Best Wishes,
Gaurav Ambwani.

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Monday, June 24, 2024 9:50 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] MRI watershed error
Sorry, I'm not sure what the problem is that you are describing. I see 
from the recon-all file that

MNI_freesurfer_T1.nii.gz is your input. What is that? Is that after skull 
stripping? Why not just give it the full head?
On 6/20/2024 3:52 PM, Gaurav Ambwani wrote:


External Email - Use Caution

Dear Freesurfer developers,

I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain 
extraction tool in 3D slicer, and then I registered it in fsl to a 
skull stripped version of a T1 weighted image of a Stroke patient 
(which I got from Openneuro).


The purpose of doing this is to, get the aseg.mgz file and overlay 
that onto the MRI of the stroke patient.


Previously I have taken the T1 1mm MNI image and received an aseg.mgz 
file which I have overlayed onto my MNI registered T1 weighted stroke 
MRI and that worked perfectly. However, This time I have taken the T1 
1mm MNI image registered that to my stroke T1 MRI, and the registered 
image hasn't gone through freesurfer.


I have attached the recon-all.log file in this email.

Freesurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1 
SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Distributor ID: Ubuntu
Description:    Ubuntu 22.04.4 LTS
Release:        22.04
Codename:       jammy

I am using a WSL in windows 11 (64 bit)

Thank you,
Best Wishes,
Gaurav Ambwani.

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Re: [Freesurfer] Recon-all manual edits - multiple re-runs

[Douglas N. Greve]

It will take all edits you have made into account when you rerun it.

On 6/25/2024 1:00 PM, Blujus, Jenna wrote:


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Hi all,

I have processed a set of T1w data through recon-all (v7.3.2) and am 
now making manual edits, if necessary. I have had a few cases where 
control points, wm.mgz, and brainmask edits are needed and 
incorporated via 'recon-all -autorecon2-cp -autorecon3 -s ${id}'. 
However, upon inspection of the updated outputs following the initial 
manual edits, further edits are required only to the wm.mgz to fix new 
topological errors.


To incorporate the second round of wm edits, would I need to rerun 
recon-all from the control point stage to incorporate */_all_/* edits 
(i.e., first round [control points, wm, brainmask]) or just from the 
wm stage with recon-all -autorecon2-wm -autorecon3 -s ${sid}? 
Essentially, I am asking if each time recon-all is re-run does it 
progressively build off of previous edits?


Let me know if you need any clarification.

Thanks in advance,
Jenna

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Re: [Freesurfer] Registering Two Anatomical Images

[Douglas N. Greve]

On 6/24/2024 6:47 PM, Andrew Jahn wrote:


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Hello,

I have a raw anatomical image called raw.mgz, which I have manually 
annotated using Freeview; the resulting annotations are saved in a 
file called seg.mgz. I want to compare this to the annotations 
automatically generated by recon-all, so I ran the image through the 
recon-all processing stream. However, the original dimensions of 
the raw.mgz image are 256x209x256, and recon-all resamples the image 
to 256x256x256 resolution.

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat


If I want to compare the amount of overlap between my annotations and 
those generated by FreeSurfer - specifically, the aparc+aseg.mgz file 
created by recon-all - what is the best way to register the seg.mgz 
file to aparc+aseg.mgz? I looked through the documentation of 
mri_vol2vol, but I wasn't sure which registration file to use. Is it 
one of the transformation files contained in the "transforms" folder 
from the image that has been processed through recon-all?

use the mri_label2vol command on that page



Thank you!

-Andy

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Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

And also don't expect the cortical surface to be very good once you get ont

On 6/24/2024 8:08 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Dear Douglas,
>
> we had checked the template and compared it to the standard template 
> (MNI152_T1_1mm_brain.nii.gz). Our template looks normal on orientation and we 
> don't see anything unusual (please see screenshot). The only difference is 
> our head is smaller (probably because it's children data).
>
> Therefore, I have two questions:
> 1. Do you think that the head size could be the reason for the reconstruction 
> failure? I don't think it should be, because the reconstruction of individual 
> data has been going very well.
> 2. After creating our template, we also used the commands below to fill holes 
> and normalize. The data type of output file is float, but we find that the 
> standard template has a data type of short. Do you think the data type might 
> influence the reconstruction? In fact, we also tried to change the datatype 
> to 'short', but there were obvious problems with the output image.
>
> # Fill holes and normalize
> fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul 
> ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats 
> ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range 
> ANTS_QS_template_MNIS.nii.gz -odt float
>
> Thank you so much!
>
> Best regards,
> Chen
>
>
> - Original Message -
>> From: "Douglas N. Greve" 
>> To: "freesurfer" 
>> Sent: Monday, 3 June, 2024 18:42:14
>> Subject: Re: [Freesurfer] Recon-all for a common template
>> Why did you do an lr reversal if it looked good? And when you say it
>> looks good, what do you mean. One thing to double check is that the
>> orientation looks ok. Load it in freeview. Up at the top you will see
>> little brain images in coronal, sagital, and axial. When you click on
>> one of those, the brain in the main image should become coronal, sag, or
>> axial. If this does not happen, then something is wrong.
>>
>> On 5/29/2024 10:47 AM, Chen Yang wrote:
>>>   External Email - Use Caution
>>>
>>> Hi Douglas,
>>>
>>> thanks so much for you reply. Yes, I checked the template and it looks 
>>> good. The
>>> orientation was in LAS originally then I did the Left-Right Reversal by 
>>> using
>>> the command "mri_convert --in_orientation RIA". Before or after the 
>>> reversal, I
>>> got the same error message. Here I attached the template, could you please 
>>> have
>>> a look in case of any clue? Thank you so much!
>>>
>>> Best,
>>> Chen
>>>
>>>
>>>
>>> - Original Message -
>>>> From: "Douglas N. Greve" 
>>>> To: "freesurfer" 
>>>> Sent: Wednesday, 29 May, 2024 15:26:25
>>>> Subject: Re: [Freesurfer] Recon-all for a common template
>>>> sounds like something is wrong with the image. Did you look at
>>>> ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
>>>> head?
>>>>
>>>> On 5/28/2024 6:07 AM, Chen Yang wrote:
>>>>>External Email - Use Caution
>>>>>
>>>>> Hi everyone,
>>>>>
>>>>> I tried to run the reconstruction with the command line:  recon-all -i
>>>>> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>>>>>
>>>>> then I got the error message:
>>>>> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>>>>> talairach_avi log file is transforms/talairach_avi.log...
>>>>> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>>>>> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64
>>>>> GNU/Linux
>>>>>
>>>>> And this is the error message in the talairach_avi.log:
>>>>> imgrege: no voxels in register
>>>>> ERROR: 'imgreg_4dfp
>>>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>>>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>>>>> talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
>>>>> status=254
>>>>> ERROR: mpr2mni305 execution aborted
>>>>>
>>>>> Does anyone know how to solve this problem? Thanks so much!
>>>>>
>>>>> Best,
>>&

Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

Sorry, I have no idea what is going wrong. Try using a full head in 
stead of skull  stripped image

On 6/24/2024 8:08 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Dear Douglas,
>
> we had checked the template and compared it to the standard template 
> (MNI152_T1_1mm_brain.nii.gz). Our template looks normal on orientation and we 
> don't see anything unusual (please see screenshot). The only difference is 
> our head is smaller (probably because it's children data).
>
> Therefore, I have two questions:
> 1. Do you think that the head size could be the reason for the reconstruction 
> failure? I don't think it should be, because the reconstruction of individual 
> data has been going very well.
> 2. After creating our template, we also used the commands below to fill holes 
> and normalize. The data type of output file is float, but we find that the 
> standard template has a data type of short. Do you think the data type might 
> influence the reconstruction? In fact, we also tried to change the datatype 
> to 'short', but there were obvious problems with the output image.
>
> # Fill holes and normalize
> fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul 
> ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats 
> ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range 
> ANTS_QS_template_MNIS.nii.gz -odt float
>
> Thank you so much!
>
> Best regards,
> Chen
>
>
> - Original Message -
>> From: "Douglas N. Greve" 
>> To: "freesurfer" 
>> Sent: Monday, 3 June, 2024 18:42:14
>> Subject: Re: [Freesurfer] Recon-all for a common template
>> Why did you do an lr reversal if it looked good? And when you say it
>> looks good, what do you mean. One thing to double check is that the
>> orientation looks ok. Load it in freeview. Up at the top you will see
>> little brain images in coronal, sagital, and axial. When you click on
>> one of those, the brain in the main image should become coronal, sag, or
>> axial. If this does not happen, then something is wrong.
>>
>> On 5/29/2024 10:47 AM, Chen Yang wrote:
>>>   External Email - Use Caution
>>>
>>> Hi Douglas,
>>>
>>> thanks so much for you reply. Yes, I checked the template and it looks 
>>> good. The
>>> orientation was in LAS originally then I did the Left-Right Reversal by 
>>> using
>>> the command "mri_convert --in_orientation RIA". Before or after the 
>>> reversal, I
>>> got the same error message. Here I attached the template, could you please 
>>> have
>>> a look in case of any clue? Thank you so much!
>>>
>>> Best,
>>> Chen
>>>
>>>
>>>
>>> - Original Message -
>>>> From: "Douglas N. Greve" 
>>>> To: "freesurfer" 
>>>> Sent: Wednesday, 29 May, 2024 15:26:25
>>>> Subject: Re: [Freesurfer] Recon-all for a common template
>>>> sounds like something is wrong with the image. Did you look at
>>>> ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
>>>> head?
>>>>
>>>> On 5/28/2024 6:07 AM, Chen Yang wrote:
>>>>>External Email - Use Caution
>>>>>
>>>>> Hi everyone,
>>>>>
>>>>> I tried to run the reconstruction with the command line:  recon-all -i
>>>>> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>>>>>
>>>>> then I got the error message:
>>>>> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>>>>> talairach_avi log file is transforms/talairach_avi.log...
>>>>> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>>>>> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64
>>>>> GNU/Linux
>>>>>
>>>>> And this is the error message in the talairach_avi.log:
>>>>> imgrege: no voxels in register
>>>>> ERROR: 'imgreg_4dfp
>>>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>>>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>>>>> talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
>>>>> status=254
>>>>> ERROR: mpr2mni305 execution aborted
>>>>>
>>>>> Does anyone know how to solve this problem? Thanks so much!
>>>>>
>>>>

Re: [Freesurfer] Calculating intensity of Individual voxel

[Douglas N. Greve]

I don't think she was responding to your question but rather to that of 
Ernest


On 6/21/2024 1:23 PM, Gaurav Ambwani wrote:


External Email - Use Caution

Dear Yujing,

I don't think that this was my question. Here are the contents of what 
I sent in my previous email:


I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain 
extraction tool in 3D slicer, and then I registered it in fsl to a 
skull stripped version of a T1 weighted image of a Stroke patient 
(which I got from Openneuro).


The purpose of doing this is to, get the aseg.mgz file and overlay 
that onto the MRI of the stroke patient.


Previously I have taken the T1 1mm MNI image and received an aseg.mgz 
file which I have overlayed onto my MNI registered T1 weighted stroke 
MRI and that worked perfectly. However, This time I have taken the T1 
1mm MNI image registered that to my stroke T1 MRI, and the registered 
image hasn't gone through freesurfer.


I have attached the recon-all.log file in this email.

Freesurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1 
SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Distributor ID: Ubuntu
Description:    Ubuntu 22.04.4 LTS
Release:        22.04
Codename:       jammy

I am using a WSL in windows 11 (64 bit)

Thank you,
Best Wishes,
Gaurav Ambwani.

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Sent:* Friday, June 21, 2024 7:46 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] Calculating intensity of Individual voxel

‘mri_info vol.mgz --voxel c r s’ will print the voxel value from col 
row slice of all frames.


Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *ERNEST KISSI

*Sent:* Friday, June 21, 2024 5:16 AM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Calculating intensity of Individual voxel

*External Email - Use Caution *

Hi, freesurfer team

Is there a way to calculate the intensity of a voxel.Let say, I have a 
voxel with coordinate 20, 30 and 34 and I wanna know the intensity of 
it. Can it be done in freesurfer?



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Re: [Freesurfer] MRI watershed error

[Douglas N. Greve]

Sorry, I'm not sure what the problem is that you are describing. I see 
from the recon-all file that


MNI_freesurfer_T1.nii.gz is your input. What is that? Is that after skull 
stripping? Why not just give it the full head?

On 6/20/2024 3:52 PM, Gaurav Ambwani wrote:


External Email - Use Caution

Dear Freesurfer developers,

I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain 
extraction tool in 3D slicer, and then I registered it in fsl to a 
skull stripped version of a T1 weighted image of a Stroke patient 
(which I got from Openneuro).


The purpose of doing this is to, get the aseg.mgz file and overlay 
that onto the MRI of the stroke patient.


Previously I have taken the T1 1mm MNI image and received an aseg.mgz 
file which I have overlayed onto my MNI registered T1 weighted stroke 
MRI and that worked perfectly. However, This time I have taken the T1 
1mm MNI image registered that to my stroke T1 MRI, and the registered 
image hasn't gone through freesurfer.


I have attached the recon-all.log file in this email.

Freesurfer version: 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1 
SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Distributor ID: Ubuntu
Description:    Ubuntu 22.04.4 LTS
Release:        22.04
Codename:       jammy

I am using a WSL in windows 11 (64 bit)

Thank you,
Best Wishes,
Gaurav Ambwani.

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Re: [Freesurfer] Renaming Freesurfer subject directories for data sharing

[Douglas N. Greve]

This can be a little tricky. Some information gets embedded into the 
files (you won't find this with a text search). You can generally see it 
with mri_info (mgz files) or mris_info (surface files)


However, mri_info can print out info that is not in the file but just 
relates to the location of the file. Eg, it prints out the "transform 
name". Eg, if you run mri_info orig.mgz you will see something like

/autofs/vast/adni3/subjects/002_S_4654.y0/mri/transforms/talairach.xfm
This gives the impression that this information is in the file, but it 
is not. If you copy orig.mgz to somewhere else and run mri_info, you 
will not see a transform name. mri_info is actually just finding the 
talairach.xfm file under the transform folder.
So if you just copy your subject to another folder, the new folder will 
appear in the transform name


If you run mris_info lh.white, you will see something like
file    : /autofs/vast/adni3/subjects/002_S_4654.y0/mri/wm.mgz
This info is embedded in the surface file. To change it, you can run 
something like

mris_convert --vol-geom ../mri/wm.mgz lh.white lh.white

Some of the info is that command lines can get embedded into files. For 
mgz files, you can run

mri_convert --delete-cmds file.mgz file.mgz
for surfaces, you can run the similar
mris_convert --delete-cmds lh.white lh.white # can be combined with 
--vol-geom above


So, my strategy would be to copy your subject folder to a new folder, 
the run mri_convert and mris_convert as above, then go through each file 
running mri_info or mris_info and looking for your original subject name.


For defacing, you can use https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace


On 6/18/2024 12:43 PM, Dan Fitch wrote:


External Email - Use Caution

Hi folks,

Our subject identifiers that we push through Freesurfer are 
internal-only. We have a public-facing set of IDs, and we'd like to 
include anonymized Freesurfer data in the BIDS that we share. So: we 
need to take the stuff we have in $SUBJECT_DIR and transform it. 
Unfortunately, this isn't as simple as just renaming the directories, 
as many of the outputs and logs include "# subjectname sub-" 
comments and cmdlines that include the subject name.


1.
Is there an extant method to rename subject directories? I've
searched around on Github and on this list's archives; came up blank.
2.
Would it be enough to walk the directories and replace all
instances of e.g. "sub-1234" with "sub-3"? Or do subject
numbers get embedded in binary headers/metadata, as well?


The extra-fun touch is that we are not actually allowed to SEE the 
mapping from internal IDs to public-facing IDs, so any tool we provide 
for this translation needs to be useable by someone who is unfamiliar 
with Freesurfer. (Don't ask.)


Then we will also need to de-face all the images, of course.

Any tips or leads appreciated; otherwise, I'll build a thing and 
eventually post about it here.


Dan Fitch
Research Engineer
University of Wisconsin-Madison Institute on Aging

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Re: [Freesurfer] Brain in a Box

[Douglas N. Greve]

You can also use mri_mask, eg, after running synthstrip, eg
mri_mask -bb 0 stripped.mgz stripped.mgz stripped.crop.mgz
-bb 0 means to create a tight (0) fitting bounding box around the 
non-zero voxels. The output stripped.crop.mgz will be the cropped output


On 6/18/2024 11:00 AM, Huang, Yujing wrote:


Hi Hebah,

You don’t need to install Surfa separately. It is part of your 
Freesurfer installation. Surfa Volume takes .mgz/.mgh, .nii/.nii.gz 
formats.


Once you sourced your Freesurfer environment, use ‘fspython’ to access 
the Python distribution shipped with your Freesurfer.


https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac

https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux

What I showed in previous message was from an interactive fspython 
session. You can write your own python scripts to use Surfa. On Surfa 
github, there are some documentations on how to use the library. In 
your sourced Freesurfer environment, use ‘fspython’ to run your scripts.


Best,

Yujing

*From:*Hebah Tanveer 
*Sent:* Tuesday, June 18, 2024 10:32 AM
*To:* Huang, Yujing 
*Subject:* Re: [Freesurfer] Brain in a Box

*External Email - Use Caution *

Hi, Yujing! I am new to the field of neuroimaging and want to better 
understand how to run Surfa. I'll need to install Python+IDE, C+IDE, 
and then run pip install surfa in my computer's command window? What 
is the file format of the slice images that Surfa will intake?



/Best,
/*Hebah*

On Tue, Jun 18, 2024 at 7:26 AM Huang, Yujing 
 wrote:


I'm wondering if the bbox() implementation in Surfa
(https://github.com/freesurfer/surfa/tree/master) will achieve the
task?

surfa.image.framed.bbox()
(https://github.com/freesurfer/surfa/blob/master/surfa/image/framed.py#L203)
computes the bounding box of the image data greater than zero.

I tried it on bert orig.mgz,

>>> import surfa as sf
>>> bert='/usr/local/freesurfer/dev/subjects/bert/mri/orig.mgz'
>>> vol=sf.load_volume(bert)
>>> vol
sf.Volume(shape=(256, 256, 256), dtype=uint8)
>>> vol.shape
(256, 256, 256)
>>> bbox=vol.bbox()
>>> bbox
(slice(47, 207, None), slice(3, 255, None), slice(3, 252, None))


Yujing

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Wighton, Paul
Sent: Monday, June 17, 2024 5:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Brain in a Box

Hi Hebah,

Interesting application.  You could try running mri_synthstrip
then analyse the resulting binary mask to determine the first and
last slices in each direction.

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Hebah
Tanveer 
Sent: Monday, June 17, 2024 5:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Brain in a Box

        External Email - Use Caution

I'm trying to determine the smallest rectangular prism that a
brain will fit in based on its MRI scan. My strategy is as
follows: I am moving through the brain axially, sagittally, and
coronally to see where the brain "starts" appearing and "stops"
appearing. Then, I'm subtracting the amount of no-brain slices
from the total number of slices and multiplying the result by the
slice thickness.

This should get me the length (sagittal plane), width (coronal
plane), and height (axial plane) of a box that contains the brain.

Is there a function within FreeSurfer that can automate this
process of determining "first and last sight of brain" ? It is
quite time consuming to manually check hundreds of patients!

Best,
Hebah


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Re: [Freesurfer] Cannot find mri/transforms/talairach.m3z file

[Douglas N. Greve]

I don't know if it is appropriate or not. The use of the synth commands 
is experimental and I was not intending for anyone to use them yet. 
That's why I put in the FS_ALLOW_DEEP hook to act as a barrier. You 
obviously have the expertise to get past that barrier, but it put you 
into a no-man's-land that we do not support./


On 6/17/2024 10:33 AM, Dan Levitas wrote:


External Email - Use Caution

Thanks, Doug.

I've spent some time trying to troubleshoot this issue, and have 
realized the following:


1). During the CROSS recon-all when I add -synthseg, no 
mri/transforms/talairach.m3z file is created in the CROSS folder.
2). During the BASE recon-all when no -synthseg is specified, a 
mri/transforms/talairach.m3z file is created in the BASE folder.
3). During the LONG recon-all (no -synthseg) specified, I'm able to 
successfully complete the process.


Is this approach (specify -synthseg only for the CROSS recon-all) 
appropriate for longitudinal processing?


On Mon, Jun 17, 2024 at 10:21 AM Douglas N. Greve 
 wrote:


Yes, that is the problem, not a lot of great options.  One thing
you could try is to  run synthmorph to create the m3z.

On 6/10/2024 2:36 PM, Dan Levitas wrote:


External Email - Use Caution

Hello,

I am following the longitudinal freesurfer pipeline
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
and getting this error on the final (LONG) portion:
/ERROR: cannot find or read transforms/talairach.m3z
/

 I can confirm that recon-all ran successfully during the CROSS
and BASE portions; it is only when I attempt to perform recon-all
-long that things fail.

My suspicion is that CA registration was not performed during
CROSS, as I used -synthseg (and -synthstrip) in that recon-all
command. I'm unsure if I need to go back and specify -careg in
the CROSS recon-all command (e.g. /recon-all -autorecon2
-careg/), or if there is some way to bypass this error. I tried
appending -nocareg to the end of my LONG recon-all command, but
this errored out with the following output:

/mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta

/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta
sub-1000_ses-2pre.long.sub-1000

will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as

/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta
reading aseg from

/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz
error:

mghRead(/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz,
-1): could not open file/


Thanks for the assistance.

Dan

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Re: [Freesurfer] How to get the parcellations to the initial space as before running recon all

[Douglas N. Greve]

hmm, not sure what is going on. I just confirmed that your command line 
works for me. Can you go into $FREESURFER/subject/bert/mri and run that 
command?


On 6/3/2024 5:47 PM, Reji, A. (Amal, Student M-EE) wrote:


External Email - Use Caution

Sir, I ran the following commands.
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o 
brain-in-rawavg.mgz --no-save-reg


mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o 
aparc+aseg_native.mgz --regheader aparc+aseg.mgz. I ran without any 
error, but when I visualize it, I cannot see the volume files in the 
native space.  I am attaching the screenshot of the same . When I 
select  show existing labels, there is no parcellation file in it.

I am mot sure what I am doing wrong.
Looking forward to hearing from you
Regards
Amal

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Monday, June 3, 2024 6:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] How to get the parcellations to the 
initial space as before running recon all
Does this web site 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat 
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat> cover 
what you need to do?


On 6/3/2024 10:58 AM, Reji, A. (Amal, Student M-EE) wrote:

*External Email - Use Caution *
Hi,
    I was trying to get the mesh files for cortical parcellations
after running recon all. I used the Ernie data set which is the
example dataset given by SimNIBS.
<https://simnibs.github.io/simnibs/build/html/dataset.html> I did
recon all to the Ernie dataset and I got the parcellations. Now I
want to get these parcellations to the same space as the space of
Ernie. How can I convert the parcellations in the initial space?
Looing forward to hearing from you
Regards
Amal Reji

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Re: [Freesurfer] Cannot find mri/transforms/talairach.m3z file

[Douglas N. Greve]

Yes, that is the problem, not a lot of great options.  One thing you 
could try is to  run synthmorph to create the m3z.


On 6/10/2024 2:36 PM, Dan Levitas wrote:


External Email - Use Caution

Hello,

I am following the longitudinal freesurfer pipeline 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) 
and getting this error on the final (LONG) portion:

/ERROR: cannot find or read transforms/talairach.m3z
/

 I can confirm that recon-all ran successfully during the CROSS and 
BASE portions; it is only when I attempt to perform recon-all -long 
that things fail.


My suspicion is that CA registration was not performed during CROSS, 
as I used -synthseg (and -synthstrip) in that recon-all command. I'm 
unsure if I need to go back and specify -careg in the CROSS recon-all 
command (e.g. /recon-all -autorecon2 -careg/), or if there is some way 
to bypass this error. I tried appending -nocareg to the end of my LONG 
recon-all command, but this errored out with the following output:


/mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta 
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta 
sub-1000_ses-2pre.long.sub-1000


will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as 
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta
reading aseg from 
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz
error: 
mghRead(/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz, 
-1): could not open file/



Thanks for the assistance.

Dan

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Re: [Freesurfer] Probability density function

[Douglas N. Greve]

I'm not sure what you mean, but I don't think we output this 
information. You can probably do it yourself in matlab or python


On 5/21/2024 12:26 PM, Jingjing Liu wrote:


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Dear Freesurfer team,
I am looking for the answer that where I can find the document of Probability 
density function in voxels of each brain volume after preprocessing. Because I 
need these indicators.

Thank you so much in advance for your reply!

Sincerely,

Jingjing Liu

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Re: [Freesurfer] BIANCA Sensitivity/Robustness to non-brain material in skull-strip

[Douglas N. Greve]

Here on the FreeSurfer list, we don't know much about the FSL tools like 
BIANCA. Why don't you post to the FSL group?


On 6/12/2024 2:51 PM, CRISTIAN MOJICA wrote:


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Hello,

I will be running BIANCA in FSL after some quality control with the 
requisite files to be listed in the Masterfile. I am examining my 
skull-strip files (in FLAIR space), and most skull strips still have 
some dura or black space occupied by CSF leftover. How sensitive is 
BIANCA to some leftover non-cortical material, or is anyone aware of 
an analysis that examines BIANCA's output as a function of 
thoroughness of skull strip, or (on the Freesurfer side) have 
suggestions for gcut or wsthresh parameters that are good for BIANCA? 
The skull strip was done in Freesurfer's recon-all process, then the 
resulting brainmask was registered into FLAIR space with FSL. Thanks 
in advance!


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Re: [Freesurfer] Does motion correction command mc-sess do censoring of high motion timepoints?

[Douglas N. Greve]

In fsfast, the censoring is done in the analysis by creating a tpexclude 
file and specifying this file when running mkanalysis-sess. Below is a 
snippet from the mkanalysis-sess --help



-tpexclude tpxfilename

This is the name of a time point exclude file (TPEF) used for removing 
outliers in the time series. The TPEF stores a list of times (in 
seconds) of time points to exclude from the analysis. The TPEF must be
found in the run directory with the functional data to which it applies. 
Like paradigm files, the TPEFs must have the same name across subjects 
and runs though their contents can differ.  Unlike paradigm
files, it is not necessary to have a TPEF in each run; if no TPEF is 
found, no time points are excluded.



On 6/11/2024 12:58 PM, Possidente, Thomas wrote:


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Hi there,

I’m using this version of Freesurfer: 
freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460


I’m using mc-sess to run motion correction on some functional task and 
resting state data. I would like to perform censoring on high motion 
timepoints in order to reduce spurious correlations due to movement 
during connectivity analysis. My main question is: does mc-sess 
include censoring? If so, what are the threshold parameters? If not, 
are there any optional arguments to turn censoring on? If not, how do 
you recommend doing motion correction with censoring using Freesurfer? 
I know mc-sess uses AFNI’s motion correction, just not sure if it 
utilizes censoring.


Thank you,

Tom


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Re: [Freesurfer] PETSurfer: pvc'ed and scaled output nifti image

[Douglas N. Greve]

It is not PVC corrected. To do that, you'd have to use the --mgx or --rbv
Note that doing voxel-wise PVC is tricky because you have multiple 
tissue types in each voxel. So you can  keep the same resolution but 
then you have to represent only one tissue type (mgx) or you have to 
create a higher resolution output volume where the resolution is high 
enough to resolve the tissue types into different volumes (rbv).


On 6/11/2024 11:11 AM, Sneha Pandya wrote:


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Dear team,

I am using mri_gtmpvc to obtain PVC’ed regional data which we will use 
as an input TAC to perform kinetic analysis.


In addition, we are also doing static SUVR analysis (sum of frames 
from 60-90 mins) in which I am scaling input PET data with gray matter 
cerebellum. In the output folder I see that upon scaling (when using 
--save-input flag) we get a scaled input image which can be used as 
SUVR. However, is this scaled image also PVC corrected or just scaled? 
If not, then is it possible to get PVC’ed and scaled nifti image?


Thank you,
Sneha


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Re: [Freesurfer] cluster area from mri_surfcluster and read_curv are inconstant

[Douglas N. Greve]

The lh.area in fsaverage is the area of the white surface (as in an 
individual subject). But the white surface is not like an individual in 
that many of the folds have been smoothed out (because it is an 
average). So mri_surfcluster fixes this internally, which is why you see 
the discrepancy (and the first method is larger than the second). If you 
want them to be identical, add --no-fix-vertex-area to mri_surfcluster.



On 6/11/2024 10:49 AM, wangzhiwei3233 wrote:


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Dear Freesurfer experts,
I got the area of a cluster by two methods, and found the results were 
inconstant.


Method 1:  During group level analysis, the individual surface was 
normalized to fsaverage. I exported the cluster area and label file by 
command /mri_surfcluster/.

The command ws as followed:
/
/
/mri_surfcluster --in ./sig.nii.gz --subject fsaverage --hemi lh 
--centroid --annot aparc --thmin ${thp} --sign ${sigsignTemp} 
--no-adjust --minarea ${tharea} --sum 
area${tharea}.${sigsignTemp}${thp_infilename}.cluster.summary --o 
area${tharea}.${sigsignTemp}${thp_infilename}.cluster.nii.gz --ocn 
area${tharea}.${sigsignTemp}${thp_infilename}.ocn.nii.gz --olab 
$Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_area${tharea}.${sigsignTemp}${thp_infilename}/label 
/


Method 2: I calculated the cluster area using  the label file outputed 
by /mri_surfcluster/ via the matlab funciton read_curv. I did this to 
test the method for calculating the area of a label manually drawn by me.

1, I first got the area of each vertex by the command
     area = read_curv('../fsaverage/surf/lh.area');
2, I red the IDs of vertices in the label file and added 1
3, I got area values of vertices in the label file and summed them.

I found the areas calculated by the Method2 were much smaller(except 
one ROI) than the ones exported by /mri_surfcluster /as shown below.


Area from Method 1：
# ClusterNo  Size(mm^2)   NVtxs   Annot
   1 *833.94* 1999     postcentral
   2 *578.52 *   1300   precuneus
   3 *243.78 *    463     middletemporal
   4 *184.72*   344   inferiorparietal
   5 *111.76*   292   insula

Area from Method 2：
ClusterNumber  Area(mm^2)  NVtxs AnotomicalRegion
1*637.39* 1999postcentral
2*480.44* 1300precuneus
3*140.37*463middletemporal
4*166.33*344inferiorparietal
5*112.76*292insula

 What's the reason? Where did I do wrong in the method 2?

Thanks.

Best,

zhiwei

--

---

Zhiwei Wang（王志伟), Associate Investigator

International Center for Primate Brain Research

Center for Excellence in Brain and Intelligence Technology

Institute of Neuroscience,Chinese Academy of Sciences

Room 215, Building #5, 500 Qiangye Road, Shanghai, 201602,China



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Re: [Freesurfer] Unequal size groups

[Douglas N. Greve]

We do not offer anything special for this. The difference in group size 
is not an issue in and of itself. The only problem that would arise is 
if the groups have different variances.


On 5/18/2024 12:07 PM, std...@virgilio.it wrote:


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Hi

I’m using fs-fast to map the connectivity differences between 3 
groups. My problem is unequally sized groups. In the sense that the 
first group consists of 40 subjects, the second of 190, and the third 
of 18. What solutions does FreeSurfer offer to handle this type of 
problem which affects the assumption of equal variances in tests like 
ANOVA?


Thanks

Stefano


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Re: [Freesurfer] Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

[Douglas N. Greve]

Mostly these:

https://pubmed.ncbi.nlm.nih.gov/15501102/

https://doi.org/10.1016/S0896-6273(02)00569-X

For a separate fornix seg, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic


On 5/22/2024 1:34 PM, Ahsan Ali wrote:


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Hello everyone,

Could anyone please help me to know which Atlas is used in the 
segmentation of corpus callosum, hippocampus, and fornix using 
freeSurfer from Brian MR images. I have gone through the literature 
but couldn't find it.


With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics (Biomedical Engineering Group)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

-- Forwarded message -
From: *Fischl, Bruce R.,PHD* 
Date: Wed, May 22, 2024, 10:52 PM
Subject: RE: Atlas Used in FreeSurfer for Segmentation of Fornix, 
Corpus Callosum, Hippocampus

To: Ahsan Ali 


Can you please post to the list so that others can answer?

*From:*Ahsan Ali 
*Sent:* Wednesday, May 22, 2024 1:04 PM
*To:* Fischl, Bruce R.,PHD 
*Subject:* Re: Atlas Used in FreeSurfer for Segmentation of Fornix, 
Corpus Callosum, Hippocampus


*External Email - Use Caution *

Dear sir,

It is not clear from these papers to me.

With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics (Biomedical Engineering Group)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

On Wed, May 22, 2024, 8:19 PM Fischl, Bruce R.,PHD 
 wrote:


Mostly these:

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://pubmed.ncbi.nlm.nih.gov/15501102/



*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://doi.org/10.1016/S0896-6273(02)00569-X



cheers

Bruce

*From:*Ahsan Ali 
*Sent:* Wednesday, May 22, 2024 4:31 AM
*To:* Freesurfer support list ;
Huang, Yujing ; Fischl, Bruce R.,PHD

*Subject:* Atlas Used in FreeSurfer for Segmentation of Fornix,
Corpus Callosum, Hippocampus

*External Email - Use Caution *

Dear FreeSurfer Team,

After reviewing the literature, I have a question: which atlases
are used in the segmentation of the fornix, corpus callosum, and
hippocampus from magnetic resonance images using FreeSurfer? This
is a significant question for me, and I would appreciate a clear
and concise answer. Please provide some relevant references.


With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics and Biomedical Engineering (AMBE)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

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.

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Re: [Freesurfer] Intensity affected after using -c flag in mri_convert

[Douglas N. Greve]

The -c means to "conform". In addition to changeing it to 1mm iso, it 
will change the data type to uchar. Uchar only has 8 bits, so it does an 
intensity rescaling to make sure all the intensities fit in this range


On 5/22/2024 12:55 PM, ERNEST KISSI wrote:


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Dear fresurfer team,

Why does the use of conform flag (-c) in mri_convert affect the 
intensity of the image?   I have an image with absolute intensity of 
1000 and after using the conform flag in mri_convert, the intensity is 
around 98.1. why is there a different scale in the intensity after the 
use of the flag?


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Re: [Freesurfer] Transformed geometry does not match

[Douglas N. Greve]

This usually means that there is a large difference in the geometry 
between time points eg, the voxel size has changed substantially. If you 
want  more help, make sure to include the recon-all.log file


On 6/7/2024 7:45 AM, Yasmine Salman wrote:


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Dear FreeSurfer developers,

I am trying to run longitudinal recon-all -long command. For some 
subject the recon-all -long command does not work and the error 
message indicate that 'transformed geometry does not match". I checked 
and the initial recon-all finished without error as well as the 
recon-all -base. I also tried to re-run de base but it does not help.
Knowing that recon-all -long command worked for the majority of my 
subjects, what can explain that it does not work for some of them ? 
And how can we solve that problem ?


Thanks in advance for your help,
Best,

Yasmine



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Re: [Freesurfer] Issue with cortical data extraction for mkanalysis-sess

[Douglas N. Greve]

Sorry, I can't understand from you description what is going wrong. How 
do you know that something is off? Can you list your command lines?


On 6/6/2024 8:22 PM, O'Dor, Sarah wrote:


We are trying to run resting state connectivity analyses using 
amygdala ROI. The left hemisphere ran fine, but for the right 
hemisphere, something is clearly off. When we export the results into 
a table, the unknown column, which should be zero, has values, and one 
of the regions instead has zeroes. It’s as if something is shifted, 
but we’ve checking the coding. Briefly, the commands we used were 
mri_vol2vol, fcseed-config, fcseed-sess, mkanalysis-sess, 
selxavg3-sess, mri_glmfit, mri_segstats. Any ideas on where/which 
commend we should be troubleshooting? We’ve run it twice and gotten 
the same results.


Thanks,

Sarah


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Re: [Freesurfer] negative values converting mgz files to nifty

[Douglas N. Greve]

That should have worked, but I would use the method on this page 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat


On 6/6/2024 4:07 PM, Nina Rouhani wrote:


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hello!

after freesurfer segmentation (through fmriprep v23), i converted the 
aparc+aseg.mgz file into a nifty file using the below code (freesurfer 
v7.4.1):

-rl $fs_dir/mri/rawavg.mgz
-rt nearest $fs_dir/mri/aparc+aseg.mgz
$sub_dir/rois/anatomical/aparc_aseg2mprage.nii.gz

however, the voxel values of the aparc_aseg2mprage.nii.gz range 
between 31000-32000 and -31000- -32000. consequently, the label values 
for particular regions no longer correspond to what’s in the 
freesurfer manuals (like those listed here: 
FsTutorial/AnatomicalROI/FreeSurferColorLUT - Free Surfer Wiki 
).


would be incredibly grateful if i could be pointed to what i’m missing 
or what could be going wrong! thank you!




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Re: [Freesurfer] Bug in mri_convert reslice-like with 4D images

[Douglas N. Greve]

Can you send us the terminal output? Can you point us to the data on the 
network so that we can recreate? @YH - can you take a look?


On 6/6/2024 3:56 PM, Iglesias Gonzalez, Juan E. wrote:


Dear FS experts,

We get a segfault when I try to resample images with the command:

mri_convert input.mgz output.mgz -rl reference.mgz

when reference.mgz has multiple frames (e.g., a RGB volume). Any idea 
of why this is happening?


Cheers,

/Eugenio (&Stefano & Pranav)


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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Douglas N. Greve]

If it is only one subject and you have no continuous variables, you can 
do it that way. If you have continuous variables, you will need to use 
DOSS (different-offset same slope) to force the slopes to be the same 
across classes (because you can't compute a slope from a single data point)


On 5/10/2024 12:46 PM, Liliana Wu wrote:


External Email - Use Caution

Thank you Douglas. That’s much clearer. I do however,  have a subject 
without a gender disclosure. Would I set up my class and contrasts as:


5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa

then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]?

Best,

Liliana


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Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

Why did you do an lr reversal if it looked good? And when you say it 
looks good, what do you mean. One thing to double check is that the 
orientation looks ok. Load it in freeview. Up at the top you will see 
little brain images in coronal, sagital, and axial. When you click on 
one of those, the brain in the main image should become coronal, sag, or 
axial. If this does not happen, then something is wrong.

On 5/29/2024 10:47 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Hi Douglas,
>
> thanks so much for you reply. Yes, I checked the template and it looks good. 
> The orientation was in LAS originally then I did the Left-Right Reversal by 
> using the command "mri_convert --in_orientation RIA". Before or after the 
> reversal, I got the same error message. Here I attached the template, could 
> you please have a look in case of any clue? Thank you so much!
>
> Best,
> Chen
>
>   
>
> - Original Message -
>> From: "Douglas N. Greve" 
>> To: "freesurfer" 
>> Sent: Wednesday, 29 May, 2024 15:26:25
>> Subject: Re: [Freesurfer] Recon-all for a common template
>> sounds like something is wrong with the image. Did you look at
>> ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
>> head?
>>
>> On 5/28/2024 6:07 AM, Chen Yang wrote:
>>>   External Email - Use Caution
>>>
>>> Hi everyone,
>>>
>>> I tried to run the reconstruction with the command line:  recon-all -i
>>> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>>>
>>> then I got the error message:
>>> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>>> talairach_avi log file is transforms/talairach_avi.log...
>>> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>>> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64
>>> GNU/Linux
>>>
>>> And this is the error message in the talairach_avi.log:
>>> imgrege: no voxels in register
>>> ERROR: 'imgreg_4dfp
>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>>> talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
>>> status=254
>>> ERROR: mpr2mni305 execution aborted
>>>
>>> Does anyone know how to solve this problem? Thanks so much!
>>>
>>> Best,
>>> Chen
>>> - Original Message -
>>>> From: "Chen Yang" 
>>>> To: "freesurfer" 
>>>> Sent: Monday, 20 May, 2024 13:59:13
>>>> Subject: [Freesurfer] Recon-all for a common template
>>>> External Email - Use Caution
>>>>
>>>> Dear Freesurfer Developers,
>>>>
>>>> my data is from 50 preschoolers and I created my own group template from 
>>>> these
>>>> kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti 
>>>> file
>>>> (see attached). Then we'd like to process this group template in 
>>>> Freesurfer to
>>>> reconstruct the cortical surfaces as the individual brain images. My 
>>>> question
>>>> is, how can i do the recon-all with the template? Because I only have this
>>>> template file I feel I don't have enough input files(?).
>>>>
>>>> Thanks in advance!
>>>>
>>>> Best regards,
>>>> Chen
>>>>
>>>> --
>>>> Chen Yang
>>>>
>>>> PhD Student
>>>> Independent Research Group 'Milestones of Early Childhood Development'
>>>> Max Planck Institute for Human Cognitive and Brain Sciences
>>>>
>>>> Email:ya...@cbs.mpg.de
>>>>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
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>>>> The informatio

Re: [Freesurfer] How to get the parcellations to the initial space as before running recon all

[Douglas N. Greve]

Does this web site 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat cover 
what you need to do?


On 6/3/2024 10:58 AM, Reji, A. (Amal, Student M-EE) wrote:


External Email - Use Caution

Hi,
    I was trying to get the mesh files for cortical parcellations 
after running recon all. I used the Ernie data set which is the 
example dataset given by SimNIBS. 
 I did 
recon all to the Ernie dataset and I got the parcellations. Now I want 
to get these parcellations to the same space as the space of Ernie. 
How can I convert the parcellations in the initial space?

Looing forward to hearing from you
Regards
Amal Reji

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Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

sounds like something is wrong with the image. Did you look at 
ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a 
head?

On 5/28/2024 6:07 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Hi everyone,
>
> I tried to run the reconstruction with the command line:  recon-all -i 
> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>
> then I got the error message:
> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
> talairach_avi log file is transforms/talairach_avi.log...
> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 
> GNU/Linux
>
> And this is the error message in the talairach_avi.log:
> imgrege: no voxels in register
> ERROR: 'imgreg_4dfp 
> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>  
> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>  talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! 
> status=254
> ERROR: mpr2mni305 execution aborted
>
> Does anyone know how to solve this problem? Thanks so much!
>
> Best,
> Chen
> - Original Message -
>> From: "Chen Yang" 
>> To: "freesurfer" 
>> Sent: Monday, 20 May, 2024 13:59:13
>> Subject: [Freesurfer] Recon-all for a common template
>
>> External Email - Use Caution
>>
>> Dear Freesurfer Developers,
>>
>> my data is from 50 preschoolers and I created my own group template from 
>> these
>> kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file
>> (see attached). Then we'd like to process this group template in Freesurfer 
>> to
>> reconstruct the cortical surfaces as the individual brain images. My question
>> is, how can i do the recon-all with the template? Because I only have this
>> template file I feel I don't have enough input files(?).
>>
>> Thanks in advance!
>>
>> Best regards,
>> Chen
>>
>> --
>> Chen Yang
>>
>> PhD Student
>> Independent Research Group 'Milestones of Early Childhood Development'
>> Max Planck Institute for Human Cognitive and Brain Sciences
>>
>> Email:ya...@cbs.mpg.de
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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>> The information in this e-mail is intended only for the person to whom it is
>> addressed.  If you believe this e-mail was sent to you in error and the 
>> e-mail
>> contains patient information, please contact the Mass General Brigham
>> Compliance HelpLine at 
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Re: [Freesurfer] Hippocampus subfield LUT

[Douglas N. Greve]

Look in $FREESURFER/FreeSurferLUT.txt
This has those indices (and a lot more). If you want just the hippo SF 
indices, you can run something like

mri_segstats --seg hipposf.mgz --ctab-default --sum sum.dat
The indices will be in sum.dat

On 5/14/2024 11:04 AM, karl landheer wrote:


External Email - Use Caution

Hello, I am looking for the LUT which converts the indices in images 
like lh.hippoAmygLabels-T.v22.mgz to region name. Is this available 
anywhere? I can’t find it


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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Douglas N. Greve]

The first one will test for a difference between group offset/intercept 
accounting for age, gender, episodes, and residuals. By setting a 
regressor contrast element to 0, one accounts for that variable because 
the variable appears in the model that is fit to the data (and so its 
effects already removed from other variables). One more thing: I would 
recommend incorporating gender in the class structure not as a 
continuous variable. So you would have 4 classes: PatentientsMale, 
PatientsFemale, HCMale, HCFemale then use contrast [0.5 0.5 -0.5 -0.5 0 
0 0 0 0 ...]


On 5/9/2024 3:26 PM, Liliana Wu wrote:


External Email - Use Caution

Hello!

I am having trouble with creating my contrast files. I did go over 
FsfdExamples (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples 
). 
However, I am unsure how should I create my contrast files if I want 
do a 2 group comparison while controlling 4 covariates:


Class:

Patients, healthy control

variables are:

Age,gender,episodes,residuals,

Here is how I set up my contrast files:

1 -1 0 0 0 0 0 0 0 0  - Contrast1 (measure group differences)

1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 
(measure group differences while accounting for covariates)


For some reason I think I am setting up those contrast files wrong… 
Any help is appreciated.


Best,

Liliana


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Re: [Freesurfer] surface and cortical thickness normalization

[Douglas N. Greve]

The reason I suggested scaling by eTIV is an analogy with a box of 
paper. The surface area of the paper in the box scales linearly with the 
volume in the box (twice the volume, twice the paper, twice the area). I 
vaguely remember doing a test of this, but, if I did, it has been a 
while. probably using eTIV^(2/3) works well too. I don't think it is so 
important that it be unitless (though maybe it is easier at review time).


On 5/3/2024 10:56 AM, Fischl, Bruce R.,PHD wrote:


Hi Yunus

I think typically you would normalize by eTIV^(2/3), which would 
result in a dimensionless scaling


Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *yunus soleymani

*Sent:* Friday, May 3, 2024 3:31 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] surface and cortical thickness normalization

*External Email - Use Caution *

Hello,

I hope you are doing well. Yesterday, I had some questions regarding 
normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I 
received answers for all of them. However, I still have one more 
question.


When I normalize brain surfaces to eTIV, they appear to be in two 
different units (mm2 and mm3). Will this be a problem? Additionally, I 
would like to know your thoughts on normalizing cortical thicknesses. 
Do you think they should be normalized to eTIV, or would it be better 
to normalize them to the mean cortical thickness of each subject?


I would greatly appreciate your response.

Thank you,
Yunus


*Yunus Soleymani*
**
*Ph.D. Candidate of Neuroimaging *
*/Tehran University of Medical Sciences/*
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+98 914 526 9298


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Re: [Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

[Douglas N. Greve]

They are not identical, for  sure. In general, I discourage people from 
modeling categorical variables (eg, Group1/2 below) as continuous 
variables because you make assumptions that might not be reasonable (eg, 
females will have twice the thickness as males). I would use the first 
method.


On 5/2/2024 8:20 PM, Lydia Chung wrote:


External Email - Use Caution

Hi FS support team,

I am going to be using mri_glmfit to test 1) main effects (which 
regions show differences in cortical thickness between group 1 and 
group 2) and 2) interaction effects (does the relationship between IV 
and DV depend on moderator). Depending on the model, the IV is 
sometimes a binary categorical variable and sometimes a continuous 
variable. The moderator is always continuous. So, interaction effects 
are either continuous x continuous OR categorical x continuous.


One thing I'm trying to understand is whether the two examples below 
are basically two different approaches that answer the SAME question: 
Do people in Group 1 differ from Group 2 on cortical thickness? 
Version 1 is the one provided by FS and Version 2 is an analog of 
another setup I have been provided by colleagues. Are these models 
answering the same or different questions? The freesurfer link below 
also shows an example of how to do an interaction (Group x Age) using 
Version 1 setup; for Version 2 setup of an interaction, I know I would 
multiply the IV and Moderator before this step so that I would have an 
additional "interaction variable" column to add as one of the 
'Variables' listed in the fsgd code.  So, I'm also curious if the two 
different methods of testing an interaction (in addition to the first 
question about the main effect) will get you the identical answer OR 
if there is something conceptually different? Do the nuances of this 
setup have to do with the difference between using DODS or DOSS?


_
_
_Main effect of Group on cortical thickness Version 1 (copied from FS 
example. link here 
)_

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables Age Weight
Input subject1 Group1 30 100
Input subject2 Group2 40 120

Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like 
an anova approach?)


_Main effect of Group on cortical thickness Version 2_
GroupDescriptorFile 1
Title OSGM
Class Subjects
Variables Group Age Weight
Input subject1 Subjects 0.5 30 100
Input subject2 Subjects -.5 40 120

contrasts: 0 1 0 0 (to test main effect of group; this feels like a 
linear regression approach?)


Thank you in advance for your help!

Lydia
--


Lydia Wu-Chung, M.A.
Doctoral candidate
BMED Lab
Department of Psychological Sciences
Rice University
6500 Main St - MS201
Houston, TX 77030
Lab Phone: 713-348-8126
Email: lydia...@rice.edu 

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Re: [Freesurfer] outcome directions of longitudinal two stage model

[Douglas N. Greve]

not sure what you mean and/or referring to. can  you elaborate?

On 5/7/2024 4:03 PM, L wrote:


External Email - Use Caution


Dear exports,

I am wondering whether the outcomes of the longitudinal two stage 
model is tp1 - tp2 or tp2 - tp1.


Thank you,

Lihong Wang

--
- Lihong


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Re: [Freesurfer] recon-all process still not finishing properly

[Douglas N. Greve]

It should just run the fill step. However, I've been slowly 
reprogramming recon-all to just see what needs to be run and rerun it, 
so you might get more than just the fill.


On 5/3/2024 4:38 PM, Dong, Yilei wrote:


External Email - Use Caution

Hi Freesurfer Developers,

Just to reply to this thread again, if I want to see if recon-all will 
just run the -fill step, do I submit it on the files that have already 
been run? In addition, does this error count as Freesurfer running out 
of RAM or it's more of a cluster issue I have to talk with the staff 
that manage it?


Sincerely,
Yilei

*From:* Dong, Yilei 
*Sent:* Tuesday, April 23, 2024 3:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly

Hi Freesurfer support,

I have several questions regarding recon-all -fill and -debug.

If we run recon-all -fill, what is the command set-up for that? From 
the ReconAllDevTable here, *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable 
<https://secure-web.cisco.com/1lmfyKn6Pvakq-RQxgJbE5k4RDGG6d0Vpvb5lGcjzph3h7UE3rIOK94h4_vGK8oa4q_FYtrbTmYfXg9SF-sFCkj4DY_oUkqnlqG_VRr6zv-uPviunfO901Vr4Llra2RZoL7k2SaVz5b8sHZwz9tr28nK4K01ItC1QwtyMTw-gA6LKU-lK3jTTjAHXqq0NK-7yqLmD6TCtsqdbNsdoxGLEfnWyV4rlB4ypTtbp8RQCkTKa8EWWLysYONW6-m24iLcIBbOt0l9i4UxjEV-DHag-8gIkxA9SeCthGdnNmHPEyy8ngikQbSR5ckvogYu-nsAi/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable>, 
do we structure the recon-all command to be: recon-all -autorecon2 
-fill -subjid ? I attempted to run recon-all -fill with -debug 
with the structure as follows: recon-all -s $subject -i $1 -fill 
-debug and I was wondering if this was the wrong format. I have also 
attached our recon-all-slurm-apr19.sb cluster submission file for 
reference.


Does recon-all -fill only run the fill step, while ignoring the 
previous steps before that or does recon-all run through all the 
initial steps including the -fill step ideally?


Regarding recon-all -debug, does the stdout file have the huge amounts 
of text specifying what each line is doing? I have included .out and 
.err files from the same recon-all -fill with -debug command for 
reference.


Sincerely,
Yilei

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, April 18, 2024 2:57 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly
not sure what is happening. You can run recon-all with -debug and 
capture the output (both stdout and stderr) into a file. This will 
cause it to print out huge amounts of text specifying what it is doing 
on each line. You should also see if there is some stderr output that 
is not being caught. You can try running recon-all -fill on the 
subject that you created to see if the fill will run at all (this may 
be easier than waiting 4 hours).


On 4/8/2024 3:18 PM, Dong, Yilei wrote:


External Email - Use Caution

Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream 
never completely finishing.
We are still encountering the same problem. For context, our 
recon-all job submission script runs recon-all for 1 image. Given a 
folder of 100 MRI images, we have another script that calls upon the 
recon-all script for each image within the folder via a for loop. The 
result is 100 jobs running in parallel on the cluster.


I have attached a screenshot of the parameters we set whenever we 
submit each recon-all job for each image by SLURM to UCSD's cluster. 
The maximum time we are allowed for each job is 48 hours. Our jobs 
are shared-node jobs, which means we run more than 1 job on a single 
node. This time, we increased RAM from 8GB to 16GB in hopes the 
entire recon-all processing stream can fully run through for each 
image, but it still stops at "mri_pretess done" and does not go on to 
the -fill step. Each job submitted to the cluster took around 4 hours 
and 20 minutes each to run in our most recent attempt.


If increasing the RAM did not change anything for us, how else can we 
get more verbose error messages? What other reasons could be why our 
recon-all aborts before finishing? I have attached a recon-all.log 
from one of our subjects for reference and a screenshot of the 
parameters we set for submitting jobs in our cluster for reference.



Freesurfer version: 7.2.0, but already available as module on UCSD's 
cluster system


Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 
28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


Recon-all

Re: [Freesurfer] brain volumes normalization

[Douglas N. Greve]

On 5/2/2024 4:03 AM, yunus soleymani wrote:


External Email - Use Caution

Hello freesurfers,

I have some questions about the output variables of Freesurfer:

1. In the case of brain volume normalization, do I need to normalize 
all the volumetric results to the eTIV or just the subcortical volumes?

All volumes. And area too as you note in #4


2. Are there any formulas other than simple division in order to 
normalize the volumes?
People will sometimes use eTIV as a regressor in the GLM instead of 
dividing (make sure to normalize so that the scale does not mess up the GLM)


3. How are the .ThckStd values (like FS_R_Insula_ThckStd) calculated? 
What does the "std" mean here?

standard deviation across vertices


4. I believe that the surface area outputs are also affected by brain 
size differences in the population. Are there any reference values in 
the Freesurfer outputs to which surface areas can be normalized?

I just use eTIV


Thank you in advance for your help.

Best regards,
Yunus



*Yunus Soleymani*
**
*Ph.D. Candidate of Neuroimaging *
/*Tehran University of Medical Sciences*/
/**/
/*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
soleymani.yu...@yahoo.com 
/

+98 914 526 9298


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Re: [Freesurfer] Figures for publication

[Douglas N. Greve]

I would use either the ocn (cluster annotation) or the cluster-wise 
corrected map: overlay as you generally don't want to show uncorrected 
data. As for the max, it is a personal choice, just what you think looks 
good or makes your point.


On 4/22/2024 7:52 AM, Asuka Toyofuku wrote:


External Email - Use Caution

Dear Freesurfer experts,

Thanks to all the help from this community, we're finally done with 
GLM analysis(mri_glimfit) and the cluster-wise correction 
(mri_glmfit_sim), and now I'm making figures for publication.


My question is

1.
Which output mgh files are commonly used for making figures for
publication? Do people use, for example,
cache.th40.abs.sig.cluster.mgh (cluster-wise corrected map:
overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values
masked by the clusters that survive correction) or even
uncorrected ones, such as sig.mgh file in the contrast directory
before running the correction? From my impression, not many people
use e.g., cache.th40.abs.sig.cluster.mgh (which shows no colour
gradation inside the clusters)...
2.
How do you select the colour-bar cut-off and max values? Most
publications I saw use min cut-off value: -log10(p) = 2.00 and
max: -log10(p) = 5.00, but some uses min: p=0.05 and max: p=0.01.
Obviously, if you set the max value (with the configure section)
very low (e.g., 2.0), the size of the cluster gets bigger and
looks more significant. Are there any suggestions for setting the
configure/threshold for the figures?


Many thanks,
Asuka



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Re: [Freesurfer] Registration in PETSurfer

[Douglas N. Greve]

bbregister is more sensitive to the smoothing in the PET images. This 
can create a confound between atrophy and registration. bbregister 
should only be used on non-smoothed data.


On 5/1/2024 5:06 AM, Ruben Dörfel wrote:


External Email - Use Caution

Hi FreeSurfer Team,

I am currently using PETSurfer to analyze FDG data. Following the 
guide *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 
, 
it is suggested that you use /mri_coreg/ to register PET and MRI 
images. However, I was wondering whether /bbregister/ might not be the 
more appropriate tool to use, especially in a case like FDG, where we 
have a lot of uptake in the brain.


Best regards,

--
Ruben Dörfel, MSc
PhD Student

Center for Psychiatry Research
Karolinska Institutet

Neurobiology Research Unit
Copenhagen University Hospital, Rigshospitalet



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Re: [Freesurfer] recon-all process still not finishing properly

[Douglas N. Greve]

not sure what is happening. You can run recon-all with -debug and 
capture the output (both stdout and stderr) into a file. This will cause 
it to print out huge amounts of text specifying what it is doing on each 
line. You should also see if there is some stderr output that is not 
being caught. You can try running recon-all -fill on the subject that 
you created to see if the fill will run at all (this may be easier than 
waiting 4 hours).


On 4/8/2024 3:18 PM, Dong, Yilei wrote:


External Email - Use Caution

Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream 
never completely finishing.
We are still encountering the same problem. For context, our recon-all 
job submission script runs recon-all for 1 image. Given a folder of 
100 MRI images, we have another script that calls upon the recon-all 
script for each image within the folder via a for loop. The result is 
100 jobs running in parallel on the cluster.


I have attached a screenshot of the parameters we set whenever we 
submit each recon-all job for each image by SLURM to UCSD's cluster. 
The maximum time we are allowed for each job is 48 hours. Our jobs are 
shared-node jobs, which means we run more than 1 job on a single node. 
This time, we increased RAM from 8GB to 16GB in hopes the entire 
recon-all processing stream can fully run through for each image, but 
it still stops at "mri_pretess done" and does not go on to the -fill 
step. Each job submitted to the cluster took around 4 hours and 20 
minutes each to run in our most recent attempt.


If increasing the RAM did not change anything for us, how else can we 
get more verbose error messages? What other reasons could be why our 
recon-all aborts before finishing? I have attached a recon-all.log 
from one of our subjects for reference and a screenshot of the 
parameters we set for submitting jobs in our cluster for reference.



Freesurfer version: 7.2.0, but already available as module on UCSD's 
cluster system


Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 
15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


Recon-all log: see attached


Thank you!


Sincerely,

Yilei


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Re: [Freesurfer] Enorm threshold for dynamic PET images

[Douglas N. Greve]

Sorry, I don't know what you mean by enorm threshold. Can you elaborate?

On 4/4/2024 4:39 PM, Sneha Pandya wrote:


External Email - Use Caution

Dear team,

I am using mc-afni2 to perform motion correction on dynamic PET images 
(ref: petsurfer wiki page). I am planning to use an average of 
un-censored frames as a template to do so. What should the threshold 
be to estimate these set of un-censored frames? For fMRI we usually 
use 0.2 or 0.3 for motion. However, for PET data we have values in the 
enorm file ranges from 0-40.


Thank you,

Sneha


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Re: [Freesurfer] GLM Using 2 Surfaces - Thickness and Area

[Douglas N. Greve]

On 4/18/2024 1:59 PM, Tejaswi D. Sudhakar wrote:


External Email - Use Caution

Hello Freesurfer team,

I am interested in doing one glm analysis using both the thickness and 
cortical surface area.


My question is two-fold:

First, is it possible to provide both the thickness and area files to 
mris_preproc and mri_surf2surf commands or is it only possible to run 
two separate glms (one for thickness and one for area)?



You must run two separate glms


Second, can we consider thickness and area as separate values or are 
they both correlated? In other words, how correlated are the thickness 
and area values?


They should be uncorrelated by construction (ie, the noise in the 
thickness should be uncorrelated from that in the area), but they may 
biologically correlated (don't know). When doing an area analysis, make 
sure to turn on jacobian correction (on by default when you spec area to 
mris_preproc) and correct for total head size. You will also need to do 
the permutation corrections for multiple comparisons (for both thickness 
and area but esp for area).


Thanks in advances,

Tejaswi


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Re: [Freesurfer] gunzip error in load_mgh.m when file path contains spaces

[Douglas N. Greve]

thanks, just checked in your change.

On 4/17/2024 9:37 PM, Tyler Slouf wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I found what I believe to be a bug. Typically I can load mgz files 
into my Matlab program without any trouble.

But if the path containing the mgz file has a space then I get an error.

When I run this very short script in Matlab calling the MRIread 
function (/Applications/freesurfer/7.4.1/matlab/MRIread.m):


filepath = char("/Users/user/Documents/folder space test/data/mri.mgz");
mri = MRIread(filepath);

I get the following error:

gunzip: can't stat: /Users/user/Documents/folder 
(/Users/user/Documents/folder.gz): No such file or directory

gunzip: can't stat: space (space.gz): No such file or directory
gunzip: can't stat: test/data/mri.mgz (test/data/mri.mgz.gz): No such 
file or directory


ERROR: problem reading fname
SWITCH expression must be a scalar or a character vector.

Error in load_mgh (line 163)
switch type

Error in MRIread (line 90)
[mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);

Error in test_load_mgz (line 2)
mri = MRIread(filepath);

I traced this down to the function *load_mgh.m 
(*/Applications/freesurfer/7.4.1/matlab/load_mgh.m) where a file path 
string
(char array) is dynamically populated with randomly generated folder 
names to unzip into.

It's about line 69 and looks like this:
[status,msg] = unix(sprintf('gunzip -c %s > %s', fname, new_fname));

You may notice that potential spaces in the path names fname and 
new_fname are not escaped with single quotes.

I edited the file to escape the parameterized strings like so:
[status,msg] = unix(sprintf("gunzip -c '%s' > '%s'", fname, new_fname));

This solved the problem for me.

Computer details:
OS: MacOS Sonoma (latest)
Chipset: Apple M1 (aarch64)
Calling Program: Matlab R2023b
Freesurfer: 7.4.1

Thank you for your time.

Sincerely,
Tyler Slouf

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Re: [Freesurfer] Skin-Skull-Brain segmentation

[Douglas N. Greve]

You can try running samseg. This will generate most of the layers you 
want, but in segmentations. You will have to convert them to surfaces 
(eg, mri_tesssellate or mri_binarize with --surf output)


On 4/15/2024 5:31 AM, XIE Jing wrote:


External Email - Use Caution

Hello all,

We would like to use FreeSurfer to remodel the head, not only 
including the detailed brain structural information, but also 
considering skin and skull. I am wondering if the FreeSurfer is 
possible to split the skin, skull and brain surfaces at the same time?


We tried the syntax "mri_make_bem_surfaces -all" , and the error notes 
were received as follows:

/nvertices=2562, nfaces=5120 /
/mri_strip_skull: triangle file 
/home/customer/Desktop/headmodel/FREESURFER/freesurfer/lib/bem/ic4.tri 
read trishrink: File 
/home/customer/Desktop/headmodel/MRI/-all/mri/brain/COR-.info not found /

/Best guess at inner_skull.tri is in inner_skull_tmp.tri/

What's your suggestions and comments on this question? We appreciate 
it very much!


Thanks in advance!
Jing
*---*
*Jing XIE*
Associate Professor
Mechatronical Engineering
Beijing Institute of Technology
Beijing 180001, PR China


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Re: [Freesurfer] surface-based filtering

[Douglas N. Greve]

Yes, you can also run
mris_fwhm --smooth-only --i input.surf-values.mgz --fwhm FWHM --s 
subject --hemi hemi --o output.surf-values-smoothed.mgz --cortex

This will give the same result as mri_surf2surf

On 4/12/2024 10:07 PM, Jiaen Liu wrote:


External Email - Use Caution

I found in the source code about the use of fwhm. It decides the 
number of iterations to achieve a gaussian filter with the specified 
fwhm in mm


Best,
Jiaen
Sent with my mobile device

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jiaen Liu 


*Sent:* Thursday, April 11, 2024 3:58:18 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

External Email - Use Caution

I thought N controls the number of smoothing iterations and the 
smoothing in each iteration is defined by fwhm which is some 
measurement of the smoothing kernel width.


Can I ask how to achieve smoothing effect similar to gaussian 
smoothing with certain sigma, where sigma is defined by voxel unit?


Thanks!

Best

Jiaen

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fischl, Bruce 
R.,PHD

*Sent:* Thursday, April 11, 2024 15:50
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

Hi Jiaen

I’m not sure what you mean by “stacked smoothing”. I think the N in 
nsmooth is the number of iterations of nearest neighbor smoothing to 
apply, which  converges to Gaussian as N gets bigger. Not sure about 
the units for fwhm – I defer to Doug on that


Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Jiaen Liu

*Sent:* Thursday, April 11, 2024 4:41 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

*External Email - Use Caution *

Hi Bruce

Thanks for your response. In the help, I found the following options. 
Is the fwhm based on voxel unit? Does nsmooth-in or-out control the 
number of stacked smoothing?


--fwhm-src fwhmsrc: smooth the source to fwhmsrc

--fwhm-trg fwhmtrg: smooth the target to fwhmtrg

--nsmooth-in N  : smooth the input

--nsmooth-out N : smooth the output

Best

Jiaen

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fischl, Bruce 
R.,PHD

*Sent:* Thursday, April 11, 2024 14:24
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

*EXTERNAL MAIL*

Yes, we support surface-based smoothing. Check out the help for 
mri_surf2surf


Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Jiaen Liu

*Sent:* Thursday, April 11, 2024 2:14 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] surface-based filtering

*External Email - Use Caution *

I’m wondering if freesurfer provides functions to filter the surface 
data within certain neighborhood exclusively on the surface. It’s 
essentially similar to regular smoothing in 3D space. But the 
filtering kernel only runs on the surface.


I can think of a solution to filter adjacent vertex in the surface 
file. But I’m not sure if the adjacent vertex is also close in space.


Thanks!

Best regards,

*Jiaen Liu Ph.D.*

Assistant Professor

*/Advanced Imaging Research Center & Radiology/*

UT Southwestern Medical Center

2201 Inwood Ln

Dallas, TX, USA, 75390

Office: 214.645.2750

Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas 

Re: [Freesurfer] BBRegistration with FSL topup

[Douglas N. Greve]

The vsm (voxel shift map) needs to be in the same voxel space as the 
fMRI (ie, it has to have the same voxel size, number of voxels, and the 
voxels must line up with the fMRI)


On 4/11/2024 8:11 PM, Gianluca Guglietti wrote:


External Email - Use Caution

Hi,

I had a question as to how to integrate fsl's topup command for 
correcting B0 distortion with freesurfer's boundary-based 
registration. I am working with high-resolution epi data (0.8mm 
isotropic) with a reduced FOV and am trying to register it to an 
MP2RAGE structural scan that I've already run through free surfer's 
recon-all. When I use the BBR command it works perfectly fine but when 
I try to add the topup field map it fails, returning this error 
"MRIvol2surfVSM: vsm dimension mismatch 1".


the field map was generated using two reverse phase encoded SE-EPI 
volumes with the same resolution and field of view as the GE-EPI BOLD 
data I am trying to register.


Any advice would be greatly appreciated!

Best,

Gianluca

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Re: [Freesurfer] vertices are -1 when using vol2label

[Douglas N. Greve]

vertices require a surface. There is no surface for cerebellum, so the 
vertices are all marked -1 to indicate that the vertex indices are not 
valid. The XYZ values are valid though


On 4/9/2024 6:36 AM, Sam W wrote:


External Email - Use Caution

Hello!
I'm trying to convert the cerebellum cortex in the aparc+aseg.mgz into 
a label so I tried:


mri_vol2label --c bert/mri/aparc+aseg.mgz --id 8 --l lh.cerebellum.label

but the resulting output file only has -1 as vertices. Is there 
anything wrong with the command above?


Best regards,
Sam

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Re: [Freesurfer] Support for GPU on Freesurfer

[Douglas N. Greve]

No, not any more. We used to have it, but it was too hard to maintain. 
You can always run in parallel on the CPU (-threads N)


On 4/3/2024 2:58 PM, Camargo, Aldo wrote:


External Email - Use Caution

Hi there,

I was wondering if there is support for GPU on FreeSurfer. I really 
would like to use it on GPU because is taking 9 hours per subject to 
recon-all.


Thanks a lot and have a nice day,

Aldo Camargo
Senior Postdoctoral Fellow at the University of Maryland, Baltimore



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Re: [Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")

[Douglas N. Greve]

You have a space in your current path (between severe and similar). That 
is causing the problem


On 4/1/2024 8:26 AM, Huang, Yujing wrote:


There is a space in your path 
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.


Rename the directory name and try again.

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *???

*Sent:* Sunday, March 31, 2024 11:18 PM
*To:* FreeSurfer 
*Subject:* [Freesurfer] recon-all mri_convert error: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")


*External Email - Use Caution *

Hello FreeSurfer Developers,

  I'm writing to ask for help while using "recon-all" command.

  I have converted some dcm format files to to nii format. Then I ran 
the command "recon-all -s maoyipeng -i 
first_sT1W_3D_TFE_tra_MR350895.nii -all", an error appeared:


/ mri_convert /home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii 
/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz //
/mri_convert: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")/

/type mri_convert -u for usage/
/Command exited with non-zero status 1/
/@#@FSTIME  2024:04:01:09:09:04 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 
100% M 5972 F 0 R 236 W 0 c 0 w 1 I 0 O 0 L 0.43 0.24 0.19/

/@#@FSLOADPOST 2024:04:01:09:09:04 mri_convert N 3 0.43 0.24 0.19/
/Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux/
/recon-all -s maoyipeng exited with ERRORS at Mon Apr 1 09:09:04 HKT 
2024 //


I've searched the list and didn't find a similar question. I'm a bit 
new to FreeSurfer, so I am unsure how to resolve this issue. I've 
attached the recon-all.log if that might help.


1) FreeSurfer 
version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
2) uname -a: Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP 
Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

3) recon-all.log: see attached


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Re: [Freesurfer] mri_volsynth fails but exits with 0 exit status

[Douglas N. Greve]

Done

On 3/29/2024 3:31 PM, Aaron Tanenbaum wrote:


External Email - Use Caution

I am currently running FreeSurfer 7.4.  I wrote a script using the 
program mri_volsynth.  I noticed for the first time the program was 
trying to write files where it did not have write permissions. It 
outputted a few error messages but gave a 0 exit status. It would be 
nice to have it exit with a nonzero exit status.


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Re: [Freesurfer] Extracting significant regions - Longitudinal two stage model

[Douglas N. Greve]

what do you mean "extract" the cluster? Do you want mean thickness for 
each cluster? Or the mean contrast? Of all the voxels in a cluster? For 
the first two, you can use something like

mri_segstats --seg clusterseg.mgz --i contrast.mgz --sum summary.txt


On 3/26/2024 9:47 AM, Liliana Wu wrote:


External Email - Use Caution

Hi,

I ran a longitudinal two stage model analysis in 83 participants 
comparing two groups. After applying cluster correction, I am seeing 
several significant regions, and I was wondering if there is a way to 
extract each significant cluster from each participant.


I appreciate any help!

Thank you,

Liliana


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Re: [Freesurfer] autorecon1 issue

[Douglas N. Greve]

What are the errors that you are facing? Can you provide more detail?

On 3/26/2024 9:12 AM, Saifullah Tumrani wrote:


External Email - Use Caution

I am using freesurfer to preprocess my t1w 3d Mris using autorecon1 
which includes first 5 preprocessing techniques till skullstripping it 
worked well for 4 different datasets including ixi one from open neuro 
SRBPS but when i am using it for another dataset which has alsmost 
same configuration it’s talairach transformation fails for some 
samples and brain matter is removed in the final brainmask.mgz file 
moreover i applied autorecon-all for this dataset and even the process 
stopped for some showing error talaraich failed and for some samples 
the whole pipeline was executed without any error but in manual 
inspection i found brain matter removed by freesurfer kindly help me 
solving this problem. I later found bad skull stripping fix at this 
link FsTutorial/SkullStripFix_freeview - Free Surfer Wiki 
 using 
some commands but i am facing errors using these command recon-all 
-skullstrip -wsthresh -clean-bm -no-wsgcaatlas -subjid skullstrip1_before


kindly look into this if you have also experience same issues or have 
any insight on this. A response will be appriciated.


Thanks


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Re: [Freesurfer] Part brain is missing

[Douglas N. Greve]

Is that an MP2RAGE? The background may be messing things up. You can try 
masking it, eg,
mri_synthstrip --i yourimage.mgz --o stripped.mgz
Then pass stripped.mgz to recon-all

On 3/25/2024 6:33 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer Developers,
>
> I am trying to do the processing for structural MRI data. I found that part 
> of brain is missing in one data (see Fig.1). Then I tried to change the 
> watershed parameter, but it didnt work at all (no matter which number I use), 
> the brainmask looks the same as before. So I did the manual editing, cloned 
> voxel from T1.mgz to brainmask.mgz. Then I run the -autorecon-pial, but it 
> froze in this step - fix topology. I checked 'wm.mgz', it contained a lot 
> skull and a lot of WM are missing (see Fig.2).
>
> I also tried to manually edit the brainmask.mgz and wm.mgz, then run 
> '-autorecon-wm' but it also froze in -fix topology. I put other might 
> relevant information in the end.
>
> I've searched in the mail archive but didn't find similar errors. I am not 
> sure if I did anything wrong. Does anyone have any thoughts on how to 
> trouble-shoot this problem? Also, Ive attached the recon-all.log in case it's 
> of any use.
>
> Thanks in advance!
>
> Best regards,
> Chen
>
>
> Other might relevant Information:
> 1) Coil element is wrong. 'HE2,4;NE2'.
> 2) I got an error message when I wad doing the recon-all first time: 
> watershed error: indices out of bounds. Then I added the command line 
> 'mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz 
> $mir/nu.mgz' based on this page 
> .
> Then I got another error message in recon-all: mri_em_register: could not 
> open brainmask.mgz so I added some cp to nu.mgz. It worked but the part of 
> brain is missing, as I mentioned in the beginning (Fig.1).
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
> 2) Platform: Linux 5.10.0-28-amd64
> 3) uname -a: Linux ramones 5.10.0-28 -amd64 #1 SMP Debian 5.10.209-2 
> (2024-01-31) x86_64 GNU/Linux
> 4) recon-all.log: see attached
>
>
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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Douglas N. Greve]

That 2mm for the gaussian is just the post-processing filter and does 
not represent the full amount of partial volume effect. What kind of 
scanner is it?


On 3/22/2024 12:42 AM, WONG Wan Wa wrote:


External Email - Use Caution

Hi Douglas,

Thanks for your clarification. This is my first time to run PetSurfer. 
We did want to normalize by cerebellar grey matter, and I will add the 
"--rescale 8 47". I just copied "6" from the example command. I know 
"6" should be the FWHM of the point-spread function (PSF) of the 
scanner as measured in image space. I did ask the technician at the 
PET centre, and he replied that the reconstruction method was "OP-OSEM 
8i21s" and the filter was "XYZ gaussian 2.00". Can I use "2" for psf 
in the command?


Thanks,
Angel


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, March 21, 2024 9:44 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied 
to PET data with single frame?
Yes, though that will normalize by the pons. If you want to normalize 
by something else, you will need to specify it with --rescale. Eg, if  
you want to normalize by ceberbellar gray matter, add

--rescale 8 47
Where did you get "6" from for the psf?

On 3/20/2024 10:57 PM, WONG Wan Wa wrote:


External Email - Use Caution

Hi Douglas,

Thanks for your reply. We used different tracers for diagnosis of AD 
or other neurodegenerative diseases, including PIB, FDG, Flutemetamol 
and TAU. If an SUV analysis is used, is it done by mri_gtmpvc? Is 
there any subsequent analysis needed?


This is my mri_gtmpvc command:

mri_gtmpvc \
  --i

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.nii.gz
\
  --reg

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.reg.lta
\
  --psf 6 \
  --seg $SUBJECTS_DIR/sub-QM001/mri/gtmseg.mgz \
  --default-seg-merge  \
  --auto-mask 1 .01 \
  --mgx .01 \
  --o $SUBJECTS_DIR/sub-QM001/pet/gtmpvc.output


Is this command okay?

Thanks,
Angel


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas 
N. Greve  <mailto:dgr...@mgh.harvard.edu>

*Sent:* Wednesday, March 20, 2024 11:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be 
applied to PET data with single frame?
you cannot apply kinetic modeling to one frame. What is you ligand? 
For a one frame acquisition, you usually use an SUV analysis.


On 3/20/2024 12:03 AM, WONG Wan Wa wrote:


External Email - Use Caution

Hi experts,

As stated in the subject, can kinetic modeling be applied to PET 
data with only one frame? Or we just stop at ROI analysis without 
kinetic modeling?


Best,
Angel


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Re: [Freesurfer] Fw: Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space

[Douglas N. Greve]

oops, should have read your 2nd email. Yes, jacobian is the reason

On 3/20/2024 5:34 AM, tyzh...@ibp.ac.cn wrote:


External Email - Use Caution

Dear FreeSurfer Experts,


Sorry, I think I've found the answer. It's because Jacobian correction 
was performed for mris_preproc, right?



Tongyu Zhang



-原始邮件-
*发件人:*tyzh...@ibp.ac.cn
*发送时间:*2024-03-20 16:31:23 (星期三)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Discrepancy between mris_preproc and mri_surf2surf results
when mapping individual's measures to fsaverage space

Dear FreeSurfer Experts,

I'm currently working on mapping cortical morphometric
measurements from each individual in the HCP dataset to the
fsaverage space.

I have noticed that both the mris_preproc and mri_surf2surf
commands can achieve this function. However, I found that the
vertex-level measurements for cortical thickness, sulcal depth,
and curvatures are consistent between these two commands, but the
results for surface area and gray matter volume are totally different.

I am puzzled by this inconsistency and speculate that perhaps
these two commands are calculated on different surfaces? I don't
understand why the two commands get different results since the
inputs are the same.

My command are as follows: (Different surface area values will be
obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files)

mris_preproc --s  id  --meas  area --target fsaverage --hemi lh
–out /Results/CorticalFeatures/id/lh.area.fsaverage.mgh

mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh
--sval /HCP/id/surf/lh.area --tval
/Results/CorticalFeatures/id/lh.area.fsaverage.gii

Thank you so much!

Tongyu Zhang


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Re: [Freesurfer] Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space

[Douglas N. Greve]

When working with area, you need to turn on jacobian correction. 
mris_preproc will do this automatically, but you have to add --jac to 
mri_surf2surf explicitly


On 3/20/2024 4:31 AM, tyzh...@ibp.ac.cn wrote:


External Email - Use Caution

Dear FreeSurfer Experts,

I'm currently working on mapping cortical morphometric measurements 
from each individual in the HCP dataset to the fsaverage space.


I have noticed that both the mris_preproc and mri_surf2surf commands 
can achieve this function. However, I found that the vertex-level 
measurements for cortical thickness, sulcal depth, and curvatures are 
consistent between these two commands, but the results for surface 
area and gray matter volume are totally different.


I am puzzled by this inconsistency and speculate that perhaps these 
two commands are calculated on different surfaces? I don't understand 
why the two commands get different results since the inputs are the same.


My command are as follows: (Different surface area values will be 
obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files)


mris_preproc --s  id  --meas  area --target fsaverage --hemi lh –out 
/Results/CorticalFeatures/id/lh.area.fsaverage.mgh


mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh --sval 
/HCP/id/surf/lh.area --tval 
/Results/CorticalFeatures/id/lh.area.fsaverage.gii


Thank you so much!

Tongyu Zhang


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Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

Oh, I see you are using 7.1.1. You can upgrade to 7.4.1. This will not 
change the basic recon-all output and you'll have access to those new 
features.


On 3/16/2024 4:21 PM, Stanica, Maria wrote:


External Email - Use Caution

We checked and the ?h.orig surface looks right. We tried the -expert 
options file that you suggested anyway, but it exited with errors 
unfortunately and didn’t work. Is there anything else we can try?


Thanks again for your help!

Best,

Maria

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Date: *Wednesday, March 6, 2024 at 9:20 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] aparc & wm underestimation

This is difficult to debug remotely. The first thing to look at is the 
?h.orig surface. Does that look more-or-less right? If not, then it 
means that the wm.mgz is wrong. If it does not look right, it means 
that the surface placement algorithm is pushing the surface into 
subcortical gray. One way to overcome this is to create a 
brain.finalsurfs.manedit.mgz by copying the brain.finalsurfs.mgz, then 
edit the brain.finalsurfs.manedit.mgz to set those areas where the 
surface is off to 255. Then create an expert options file with

WhitePreAparc --rip-bg-no-annot --restore-255  --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option

On 3/5/2024 7:10 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Yes, the problem is that the white surface on the left side of the
image is extending too far into subcortical gray matter. We did
delete the control points and ran some white matter edits, but the
image I sent you is after we applied those edits (it was even
worse before). I don’t see any other wm edits we can make to the
image. It didn’t resolve our issue enough to make the image usable
for our analyses, so I wanted to see if there was anything else we
could do to resolve the problem.

Thank you!

*From: *freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Just to make sure I understand, the problem is that the white
surface on the left side of the image is extending too far into
subcortical gray matter, right? This can be difficult to fix, but
the right fix is to edit the wm.mgz. Make sure to delete your
control points as that is not the right fix. Also, remember that
the surfaces in this area may always be inaccurate if you can see
where the boundary is.

On 3/3/2024 6:09 PM, Stanica, Maria wrote:

*External Email - Use Caution *

This is after the most recent round of edits for one of the
subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

*From: *freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all.
Everything processed correctly (and exited without
errors), except 4 images which have an underestimation in
coronal subcortical region. The underestimation is
significant and goes on for about 10-12 slices (for one
image it was 153-162, for another it was 150-164).

After searching the list, we attempted control points,
which ended up not working (I don’t believe this was the
right method to correct the error). Then we tried white
matter edits, and one of the images was resolved, but the
other 3 did not get better. Is there anything else we
could do to try to resolve the issue? I can provide any
other information needed. Any help would be appreciated!

 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 

Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Douglas N. Greve]

Yes, though that will normalize by the pons. If you want to normalize by 
something else, you will need to specify it with --rescale. Eg, if  you 
want to normalize by ceberbellar gray matter, add

--rescale 8 47
Where did you get "6" from for the psf?

On 3/20/2024 10:57 PM, WONG Wan Wa wrote:


External Email - Use Caution

Hi Douglas,

Thanks for your reply. We used different tracers for diagnosis of AD 
or other neurodegenerative diseases, including PIB, FDG, Flutemetamol 
and TAU. If an SUV analysis is used, is it done by mri_gtmpvc? Is 
there any subsequent analysis needed?


This is my mri_gtmpvc command:

mri_gtmpvc \
  --i

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.nii.gz
\
  --reg

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.reg.lta
\
  --psf 6 \
  --seg $SUBJECTS_DIR/sub-QM001/mri/gtmseg.mgz \
  --default-seg-merge  \
  --auto-mask 1 .01 \
  --mgx .01 \
  --o $SUBJECTS_DIR/sub-QM001/pet/gtmpvc.output


Is this command okay?

Thanks,
Angel


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Wednesday, March 20, 2024 11:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied 
to PET data with single frame?
you cannot apply kinetic modeling to one frame. What is you ligand? 
For a one frame acquisition, you usually use an SUV analysis.


On 3/20/2024 12:03 AM, WONG Wan Wa wrote:


External Email - Use Caution

Hi experts,

As stated in the subject, can kinetic modeling be applied to PET data 
with only one frame? Or we just stop at ROI analysis without kinetic 
modeling?


Best,
Angel


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Re: [Freesurfer] What do the stats files tell us?

[Douglas N. Greve]

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

On 3/18/2024 4:38 PM, Vivek Kandasamy wrote:


External Email - Use Caution

Hello,

So I ran FreeSurfer to get numeric data from MRI images and got these 
files under the stats page.


Screenshot 2024-03-18 144107.png

Do you know what each file tells us about our MRI images such as 
the lh.aparc.DKTatlas.mapped, lh.BA_exvivo.stats, lh.BA_exvivo.thresh, 
lh.curv, lh.w-g.pct, and wmparc.DKTatlas.mapped files?


Thanks,

Vivek Kandasamy

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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

What is your fcseed-config command line? If the input is not fmcpr, then 
you have to set the input when you config, eg, -funcstem f.even


On 3/19/2024 11:37 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

Thank you Doug.
The preproc-sess command line runs fine.
An error occurs on:
fcseed-sess -s ID -cfg wm.config -overwrite
ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr

Best regards
Stefano

Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve 
 ha scritto:


Hi Stefano, I think I found and fixed the problem. Can you try these?

On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

Hi Doug,

The raw functional file is firstly passed with motion correction 
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.

Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:

preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 
-fsd rest -per-run -sliceorder even -force


There are issues with labels since excluding motion correction 
doesn't produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, 
which cannot be found because it is not created using the -nomc option.


When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and 
rerun preproc, the operation is done and the 
fmcpr.odd.sm0.fsaverage.lh is created.


However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
-overwrite), a second error occurs (reported below) because the 
script searches for fmcpr, which cannot be produced since I used -mc.


ERROR: could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr 
This error seems to be related to the script searching for the fmcpr 
file, which isn't available due to the use of -mc.


Thank you.

Best regards,


Stefano




Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
 ha scritto:


Hi Doug have you any news
Thank you very much!
Stefano

Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
 ha scritto:


Thank you.
I’m attaching the file.
Stefano


Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
 ha scritto:


can you send me this file 
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess



On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

It seems to me that I've done what you suggest. Attached is a 
new outputs.

Thanks
Stefano

Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
 ha scritto:


Are you sure that you are using the new version that I gave 
you? It looks like the previous version. Also, it does not look 
like the entire terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


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The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output




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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Douglas N. Greve]

you cannot apply kinetic modeling to one frame. What is you ligand? For 
a one frame acquisition, you usually use an SUV analysis.


On 3/20/2024 12:03 AM, WONG Wan Wa wrote:


External Email - Use Caution

Hi experts,

As stated in the subject, can kinetic modeling be applied to PET data 
with only one frame? Or we just stop at ROI analysis without kinetic 
modeling?


Best,
Angel


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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

Hi Stefano, I think I found and fixed the problem. Can you try these?

On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

Hi Doug,

The raw functional file is firstly passed with motion correction 
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.

Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:

preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 
-fsd rest -per-run -sliceorder even -force


There are issues with labels since excluding motion correction doesn't 
produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, which 
cannot be found because it is not created using the -nomc option.


When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and 
rerun preproc, the operation is done and the 
fmcpr.odd.sm0.fsaverage.lh is created.


However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
-overwrite), a second error occurs (reported below) because the script 
searches for fmcpr, which cannot be produced since I used -mc.


ERROR: could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr 
This error seems to be related to the script searching for the fmcpr 
file, which isn't available due to the use of -mc.


Thank you.

Best regards,


Stefano




Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
 ha scritto:


Hi Doug have you any news
Thank you very much!
Stefano

Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
 ha scritto:


Thank you.
I’m attaching the file.
Stefano


Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
 ha scritto:


can you send me this file 
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess



On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

It seems to me that I've done what you suggest. Attached is a new 
outputs.

Thanks
Stefano

Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
 ha scritto:


Are you sure that you are using the new version that I gave you? 
It looks like the previous version. Also, it does not look like 
the entire terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


External Email - Use Caution

The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output




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#! /bin/tcsh -f

#
# preproc-sess - runs preprocessing (mc, spatsmooth, mkbrainmask, inorm)
#
# Original Author: Doug Greve
#
# Copyright © 2021
# The General Hospital Corporation (Boston, MA). 
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-b...@nmr.mgh.harvard.edu
#

# To get per-run reg with smoothing, make sure -fwhm is after -per-run:
# preproc-sess -s risk001 -per-run -fwhm 5 -fsd bold 
# This creates fmcpr.sm5, then
# mkanalysis-sess -native -funcstem fmcpr.sm5 ...

set VERSION = 'preproc-sess @FS_VERSION@';

set inputargs = ($argv);
set DateStr = "`date '+%y%m%d%H%M'`"

set instem   = ();
set mcinstem   = ();
set mcoutstem  = ();
set stcinstem   = ();
set stcoutstem  = ();
set sminstem   = ();
set smoutstem  = ();
set inormstem  = ();
set maskdir= masks
set maskstem   = brain;
set UseSmoothMask = 0;
set fwhm = ();
set surffwhm = ();
set volsurffwhm  = (); # for testing
set

Re: [Freesurfer] Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1

[Douglas N. Greve]

I've looked into this a little bit.
I looked at the area of the original manual labels for entorhinal as 
found in the aparc. They do show a lh>rh asym of 3%, but it is not 
significant (p=.45).
I looked at the automatic labels in two other large data sets. I found 
significant lh>rh asym of ento area in both of about 8-10%.
I don't consider 10% asym in area to be a symptom of something 
problematic. This would represent an expansion or contraction of the 
entorhinal border of about 0.5mm. I'm guessing that this is beyond the 
accuracy that we can expect.
I was looking at surface area, but now I see that you are looking at 
volume. The manual labels were defined on an areal basis, and I assume 
that that was the basis of the volume asym, but it could be due to 
differences in thickness.
How big a difference are you seeing in volume? Can you look at area and 
thickness to see if you see differences there?
Also, the surfaces are really hard to place in this area. Oftentimes, 
the ento will have a big bite in it that has to be fixed manually. I 
don't think there is asym in the bites, but it could make a particular 
case look extreme.
In general, we don't recommend doing laterality studies with the aparc 
as none of the steps involved have been developed to make sure that 
laterality artifacts are removed. In this case, it sounds like you are 
checking laterality for QA purposes?



On 3/13/2024 9:30 PM, Katie Vandeloo wrote:
>  External Email - Use Caution
>
> Hi Dr. Greve,
>
> I hope you are doing well. I am hoping to get in touch with someone from MGH 
> about some issues with Freesurfer 7. Our group hasn’t yet been successful in 
> finding the right person to talk to about this!
>
> We noticed that there are large discrepancies between left and right 
> hemisphere volumes of the perirhinal cortex (exceptionally small volumes in 
> the right hemisphere) in the outputs of recon-all for Freesurfer 7 but NOT 
> Freesurfer 6. I have reached out to other labs who observed the same pattern. 
> I think there is something systemic about Freesurfer 7 that should be looked 
> into. Just wanted to make someone aware - please let me know if there is 
> someone else I should contact about this.
>
> Thank you for your time!
>
> Kind Regards,
> Katie Vandeloo

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Re: [Freesurfer] GCS file format specification and conversion to GIFTI

[Douglas N. Greve]

It is not really something that can be converted to an overlay (gifti or 
otherwise). It is a probabalistic atlas with prior probabilities for 
each label as well as curvature mean and stddev for each label at each 
point in space. If you know some C++, you can look at GCSAread() in 
gcsa.cpp to see what gets read in.


On 3/13/2024 7:00 AM, Oscar Esteban wrote:


External Email - Use Caution

Dear all,

I'm trying to understand the GCS file format as I failed to try an 
easy conversion with mris_convert.


If mris_convert cannot convert GCS to GIFTI, is there any open 
description of how the format is implemented?


Thanks very much

Best,
Oscar

*___*
*Oscar Esteban, Ph.D.*
Research and Teaching Ambizione FNS Fellow
Dept. of Radiology, CHUV, University of Lausanne

+41 77 957 00 77
+1 (650) 733 33 82

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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

Are you sure that you are using the new version that I gave you? It 
looks like the previous version. Also, it does not look like the entire 
terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


External Email - Use Caution

The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output


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Re: [Freesurfer] Trouble Project Surface Annotation to Volume

[Douglas N. Greve]

Hi Bram, try using mris_surfseg2vol. Look in the recon-all log file for 
an example usage

doug


On 3/10/2024 12:43 PM, Bram Diamond wrote:


External Email - Use Caution

Hello FreeSurfer Experts!

I’m having trouble projecting the Yeo 17n annotation to volume space. 
I’ve tried on FS v7.4.1 on Mac OS (14.3.1) and FS v7.3.2 on Linux (7.9).


I’ve tried the following two methods:

 1. aparc2aseg 

cd $FREESURFER_HOME/subjects/fsaverage/label

mri_aparc2aseg \

--s fsaverage \

--o Yeo2011_17Networks_N1000.mgz \

--annot Yeo2011_17Networks_N1000

 Output 

SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects

subject fsaverage

outvol Yeo2011_17Networks_N1000.mgz

useribbon 0

baseoffset 0

RipUnknown 0

Reading lh white surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white

Reading lh pial surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.pial

Loading lh annotations from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot


Have color table for lh white annotation

Building hash of lh white

Building hash of lh pial

Reading rh white surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.white

Reading rh pial surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.pial

Loading rh annotations from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot


Have color table for rh white annotation

Building hash of rh white

Building hash of rh pial

Loading ribbon segmentation from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz


Loading aseg from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/mri/aseg.mgz


ASeg Vox2RAS: ---

-1.0   0.0   0.0   128.0;

 0.0   0.0   1.0  -128.0;

 0.0 -1.0   0.0   128.0;

 0.0   0.0   0.0   1.0;

-

Labeling Slice (256)

  0 1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 16  17  
18  19


 20 21  22  23  24  25  26  27  28  29  30  31  32  33  34  35 36  37  
38  39


 40 41  42  43  44  45  46  47  48  49  50  51  52  53  54  55 56  57  
58  59


 60 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 76  77  
78  79


 80 81  82  83  84  85  86  87  88  89  90  91  92  93  94  95 96  97  
98  99


100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 
117 118 119


120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 
137 138 139


140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 
157 158 159


160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 
177 178 179


180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 
197 198 199


200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 
217 218 219


220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 
237 238 239


240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 
332584


Used brute-force search on 0 voxels

Writing output aseg to Yeo2011_17Networks_N1000.mgz

error: mghWrite(Yeo2011_17Networks_N1000.mgz, -1): could not open file

#VMPC# mri_aparc2aseg VmPeak  0

mri_aparc2aseg done

 2. label2vol 

cd $FREESURFER_HOME/subjects/fsaverage/label

mri_label2vol \

--annot lh.Yeo2011_17Networks_N1000.annot \

--o lh.Yeo2011_17Networks_N1000.mgz \

--hemi lh \

--fill-ribbon \

--identity \

--subject fsaverage

 Output 

Number of labels: 0

Annot File:      lh.Yeo2011_17Networks_N1000.annot

Template Volume: (null)

Outut Volume: lh.Yeo2011_17Networks_N1000.mgz

Registration File: (null)

Fill Threshold: 0

Label Vox Vol:  1

ProjType:       (null)

ProjTypeId:     0

ProjStart:     0

ProjStop:       0

ProjDelta:     0.1

Subject: fsaverage

Hemi:     lh

UseNewASeg2Vol: 0

DoLabelStatVol 0

LabelCodeOffset 0

setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects

7.4.1

INFO: loading surface 
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white


nvertices = 163842

Reading thickness 
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.thickness


Loading annotations from lh.Yeo2011_17Networks_N1000.annot

annotidmax = 18

nlabels = 18

Loading /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz

Mapping

error: mghWrite(lh.Yeo2011_17Networks_N1000.mgz, -1): could not open file



I’ve done this before, so I feel like I must be doing something wrong. 
Any ideas?


Cheers,

Bram

*Bram R. Diamond, MS*

Clinical Psychology Doctoral Candidate

Northwestern University Feinberg School of Medicine

Mesulam Center for Cognitive Neurology & Alzheimer’s Disease

300 E. Superior Street | Tarry 8 | Chicago, IL 60611

www.brain.northwestern.edu


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Re: [Freesurfer] Cortical parcellation showing dots

[Douglas N. Greve]

And how does the parcellation look on the surface?

On 3/7/2024 9:53 AM, Hyunchul Lee wrote:


External Email - Use Caution

Yes, it looks fine to me
Those dots seem to lie on the pial surface

On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve 
 wrote:


Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I'm using Freesurfer recon-all to create reconstructions to use
with MNE-python for source estimation of SEEG data. My work
relies on having correct labeling of segmentation data. For most
cases, there has been no trouble but I am having trouble where
the cortical parcellation shows up as dots in one hemisphere.
Please see image attached. I also noticed that the lh.ribbon.mgz
is also 'dotty' (also attached). There is no issue with the right
hemisphere. This reconstruction was not manually edited, but only
recon-all was used.

I have tried using mris_volmask --label_left_ribbon, setting the
argument to various values. That didn't work that great -
reducing to 0 basically whites everything out except for the
white matter on the ipsilateral hemisphere and anything 1 or more
produces the same 'dots'. Interestingly the pial and wm surfaces
all look ok. Also, I am not sure if creating the correct
ribbon.mgz is going to fix the aparc.a2009+aseg file.

I would really appreciate your advice.

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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Re: [Freesurfer] Cortical parcellation showing dots

[Douglas N. Greve]

Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I'm using Freesurfer recon-all to create reconstructions to use with 
MNE-python for source estimation of SEEG data. My work relies on 
having correct labeling of segmentation data. For most cases, there 
has been no trouble but I am having trouble where the cortical 
parcellation shows up as dots in one hemisphere. Please see image 
attached. I also noticed that the lh.ribbon.mgz is also 'dotty' (also 
attached). There is no issue with the right hemisphere. This 
reconstruction was not manually edited, but only recon-all was used.


I have tried using mris_volmask --label_left_ribbon, setting the 
argument to various values. That didn't work that great - reducing to 
0 basically whites everything out except for the white matter on the 
ipsilateral hemisphere and anything 1 or more produces the same 
'dots'. Interestingly the pial and wm surfaces all look ok. Also, I am 
not sure if creating the correct ribbon.mgz is going to fix the 
aparc.a2009+aseg file.


I would really appreciate your advice.

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

[Douglas N. Greve]

Yujing, you can just send Taylor a binary that can be put in the local 
version of $FREESURFER/bin


On 3/6/2024 11:45 AM, Huang, Yujing wrote:


Hi Taylor,

Thanks for sharing the data.

I see the problem now.  The first 14336 bytes of your rh.area fit 
SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of 
MRI_CURV_FILE.


We will have a fix in dev version. But I’m not sure how to get around 
this in FS 7.2.


Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Wednesday, March 6, 2024 9:47 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


*External Email - Use Caution *

Hello Yujing,

If I rerun this command:

mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

It says it is writing curvature file in the command line output:

writing curvature file ../surf/rh.area

Though the problem persists (mri_info says same thing as before). I 
have attached rh.white and rh.area for your review.


Many thanks,

Taylor

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Date: *Wednesday, March 6, 2024 at 8:37 AM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


It doesn’t look like rh.area is recognized correctly. ‘mri_info 
rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 
dimensions.


I’m not sure where exactly the area values are calculated. What happen 
if you re-run this step?


mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

Can you share the ?h.white and ?h.area?

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Tuesday, March 5, 2024 7:24 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


*External Email - Use Caution *

Hello Yujing,

Thank you for your quick response!

When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial


I get the following error:

error: No such file or directory

error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): 
could not open file


error: No such file or directory

error:

mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area

        type: unknown

  dimensions: 831 x 10015 x 25953

voxel sizes: -0.00, -0.00,    nan

        type: SHORT (4)

        fov: 1016.473

        dof: 1

      xstart: 0.0, xend: 990983162970892849632569550308376576.0

      ystart: -0.0, yend: 3079152361728581627851833344.0

      zstart: -0.0, zend: -3815443229699337177012458129513775104.0

          TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 
0.00 degrees


    nframes: 1

    PhEncDir: UNKNOWN

    FieldStrength: 0.00

ras xform present

  xform info: x_r =  -1., y_r =   0., z_r = 0., c_r = 
-18770011487391973376.


            : x_a =   0., y_a =   0., z_a = 1., c_a =      
  nan


            : x_s =   0., y_s =  -1., z_s = 0., c_s =    
-0.


Orientation   : LIA

Primary Slice Direction: coronal

voxel to ras transform:

              0.  -0.      nan        nan

            -0.  -0.      nan        nan

            -0.   0.      nan        nan

              0.   0.   0.     1.

voxel-to-ras determinant nan

ras to voxel transform:

error: mat = NULL!

It appears that this is where the issue is coming from. Any ideas on 
why this is occurring? The brain is normal and has good rh.white and 
rh.pial surfaces.


Many thanks,

Taylor

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Date: *Tuesday, March 5, 2024 at 4:25 PM
*To: *Freesurfer support list 
*Subject: *[EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc 
could not establish read access to rh.area


*CAUTION:*This email originated from outside the organization. *DO NOT 
CLICK ON LINKS* _or_ *OPEN ATTACHMENTS* unless you know and trust the 
sender.


Hi Taylor,

I don’t understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.


Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ 
directly? Pass full path to your rh.area and rh.area.pial.


What does ‘mri_info rh.area’ report?

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Tuesday, March 5, 2024 2:35 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] recon-all hard error: mris_calc could not 
establish read access to rh.area


*External Email - Use Caution *

Hello FreeSurfer Developers,

I am attempting