[Freesurfer] Cortical Thickness Measures for MTL

[Kidwai, Ambereen]

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Hello,

I have been manually tracing the entorhinal cortex, dividing it into the 
antero-lateral entorhinal and posterior-medial entorhinal cortex. I am looking 
for a way to get cortical thickness measures for this region. I have a few 
questions relating to this:


  1.  Is it possible to import my manually traced labels (traced in ITK-snap) 
into freesurfer and then get the thickness measures for these labels?
  2.  Is it possible to edit the aparc or aseg in order to divide the 
entorhinal cortex into the two regions that I am delineating?
  3.  If neither of the above options are possible, is there any other way to 
get cortical thickness measures for manual segmentation of this region?

I appreciate any help or insight you can give me.

Best regards,

Amber Kidwai
Research Assistant
Functional Neuroimaging of Memory Laboratory
Center for Vital Longevity | University of Texas at Dallas
1600 Viceroy Drive Suite 800 Dallas, TX 75235
Cell: (214) 675 3612
[Description: Description: CVL_logo]




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[Freesurfer] nalysis of covariance between functional connectivity data (FS-FAST) and cortical thickness

[stdp82]

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Hi,

how can I perform vertex by vertex (surface) analysis of covariance between 
functional connectivity data (FS-FAST) and cortical thickness, regressing out 
the effect of groups?

My mean concern is how buid the fsgd file.

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Re: [Freesurfer] Error/shifting in cortical parcellation

[Douglas N. Greve]

Can you try an experiment for me?
cd $SUBJECTS_DIR/subject/surf
cp lh.sphere.reg lh.sphere.reg.auto # make a backup
mris_register -norot -rotate 0 0 +15 -curv rh.sphere 
$FREESURFER_HOME/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif 
rh.sphere.reg

Then run
recon-all -s subject -autorecon3 -nosphere -nospherereg
And see if that fixes the problem

ps. It looks like you are using a development of FS from Jan 11, 2020. 
In general, you should only use released versions



On 6/1/2021 5:10 AM, Helena-Céline Stevelt wrote:

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Dear Freesurfer Community,

I wish to manually reassign/edit cortical parcellation performed by FS.

We use the cortical parcellation done by FS and it has worked very 
well for most of our subjects. However, we have two subjects where the 
parcellation has not been done correctly. It seems that the central 
sulcus has been mis-classified to be one sulcus too far posterior in 
the brain - this has resulted in incorrect labeling of surrounding 
gyri. Curiously, it is only one hemisphere for both subjects (rh for 
one and lh for the other), where the other hemisphere is correctly 
parcellated.


In our two mis-parcellated subjects, how might we manually reassign or 
guide FS to correctly classify the central sulcus and thus correctly 
label the surrounding gyri?


I have attached a picture of an erroneous parcellation.
Freesurfer version: freesurfer-linux-centos6_x86_64-dev-20201011-4d2b06a
Platform: Ubuntu 16.04

Best,
Helena-Céline Stevelt
Danish Research Centre for Magnetic Resonance

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Re: [Freesurfer] Tracula registration failure

[Yendiki, Anastasia]

Hi Marena - If the registration between the diffusion and T1 images is 
reasonable, this should work. You should bypass any pathways that lie mostly in 
the truncated part of the diffusion scans.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Marena Manierka 

Sent: Wednesday, June 2, 2021 12:28 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula registration failure


External Email - Use Caution

Hello Anastasia,

Not sure if you've had a chance to look at my previous message. I've manually 
gone through the registrations of all the subjects in my dataset now in 
Freeview. Although the anatomical scans appear to be complete, the dtifit 
images show significant clipping of the temporal lobes in almost every 
individual (even those scans where tracula prep, bedp and path steps worked 
without casting an error). Is it still possible for me to run tracula on this 
dataset? Should I be re-processing all subjects with the config file set up to 
exclude the ILF tracts, or can I pull the data and simply exclude those tracts 
running through temporal lobes in my final analysis?

Any advice would be greatly appreciated. I'm new to this type of analysis and 
no one in my lab has published using TRACULA previously.

Thanks very much,
Marena

On Wed, May 26, 2021 at 1:47 PM Marena Manierka 
mailto:marena.manie...@gmail.com>> wrote:
Hi Anastasia,

Thank you so much for your reply. I noticed the truncated temporal lobes in the 
registered dti_FA.bbr, but I do not see the same problem in either the T1.mgz 
or the aparc+aseg.mgz when loaded into freeview. In the subject's native space 
diffusion weighted image (dtifit_FA.nii.gz) it does seem like a portion of the 
temporal lobes is cut off.

Let me know if there are other files/ screenshots I can provide to help with 
solving this issue.

Best,
Marena

On Wed, May 26, 2021 at 1:04 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Marena - How does the T1 of this subject and its freesurfer segmentation 
(aparc+aseg) look? In the image the brain looks truncated, is that the case 
with the T1?

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Marena Manierka 
mailto:marena.manie...@gmail.com>>
Sent: Tuesday, May 25, 2021 8:47 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula registration failure


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To the Tracula team:

I am attempting to complete my first project using the Tracula pipeline on a 
mixed dataset of autism, schizophrenia, and control adult brains. I ran the 
tracula prep, bedp and path steps for the autistic subject in question without 
receiving any error messages. However, when I attempt to view the registration 
of the FA.bbr.nii.gz image to the MNI brain the registered image appears as a 
completely white, roughly brain-shaped mask. This has not occurred with other 
subjects from the dataset. I have attached a screenshot from freeview for 
reference.
When I load the subject's dtifit_FA.nii.gz in freeview it appears to be 
relatively normal. Is this a fatal error in the registration process, and is 
there any way to correct it?
I have also attached the log file for the subject in case this is helpful.

Thank you for your help,
Marena


--
Marena Manierka, B.Sc
Graduate Student, Integrative Program in Neuroscience
Department of Psychology, MSS 414/ MS0296
University of Nevada, Reno
marena.manie...@gmail.com
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Re: [Freesurfer] Recon-all running on a loop

[Hoopes, Andrew]

Hi Diana,

If there are a lot of obvious holes in the surface topology, it might be worth 
doing some manual fixing of the white-matter segmentation. The tutorial at 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 walks 
through that process.

Best
Andrew

From: DIANA ORTEGA CRUZ <100315...@alumnos.uc3m.es>
Date: Thursday, May 27, 2021 at 3:32 AM
To: Freesurfer support list , Hoopes, Andrew 

Subject: Re: [Freesurfer] Recon-all running on a loop

External Email - Use Caution
Dear Andrew,

Thank you for your reply. I shared with you the recon-all.cmd file via Drive, 
since I could not upload it directly to the mail. I also copy here (down) the 
last lines in this file.

I checked the resulting volumes and surfaces up to that point and the 
smoothwm.nofix surfaces look like they have a lot of holes, which I understand 
could cause the error. I also run again recon-all for that subject without 
parallelizing as you advised, but the process was again stuck at the same step.

Do you think it would be possible to change anything in the original file or 
the recon-all configuration to fix this issue?

Thanks a lot for your help!!! Best,
Diana

#@# Fix Topology rh Tue May 18 04:37:48 UTC 2021
 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig 
orig.nofix -out orig.premesh -ga -seed 1234 NoUMA0233 rh
 mris_euler_number ../surf/lh.orig.premesh
 cp ../surf/lh.orig.nofix ../surf/lh.orig.premesh
 mris_euler_number ../surf/rh.orig.premesh
 cp ../surf/rh.orig.nofix ../surf/rh.orig.premesh
 cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
 cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
 mris_topo_fixer -orig_name orig.nofix -out_name orig.premesh -mgz -warnings 
-seed 1234 NoUMA0233 lh
 cp ../surf/rh.qsphere.nofix ../surf/rh.qsphere
 cp ../surf/rh.smoothwm.nofix ../surf/rh.smoothwm
 mris_topo_fixer -orig_name orig.nofix -out_name orig.premesh -mgz -warnings 
-seed 1234 NoUMA0233 rh

 mris_remesh --remesh --iters 3 --input 
/media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/lh.orig.premesh
 --output 
/media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/lh.orig

 mris_remesh --remesh --iters 3 --input 
/media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/rh.orig.premesh
 --output 
/media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/rh.orig
F

El mié, 26 may 2021 a las 1:59, Hoopes, Andrew 
(mailto:ahoo...@mgh.harvard.edu>>) escribió:
Hi Diana,

Can you send the recon-all.cmd file? Have you tried running without parallel 
processing enabled?

Best,
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of DIANA ORTEGA CRUZ 
<100315...@alumnos.uc3m.es>
Date: Friday, May 21, 2021 at 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Recon-all running on a loop

External Email - Use Caution
Dear FreeSurfer team,

My name is Diana Ortega, I am a Neuroscience PhD student at Universidad 
Politécnica of Madrid. I run a job to compute recon-all in parallel for 30 
subjects remotely on a supercomputer at my research institution. This job 
finished due to timeout, and all subjects but one finished without errors. 
However, one of the subjects was not finished and it appears as if it was stuck 
on a loop. Its recon-all.log is constantly adding new lines (the file is 20GB 
in size), and from recon-all-status.log it appears to be stuck in the "Fix 
Topology" step. Have you ever encountered a similar situation? Would you know 
why this could have occurred?
Here are the details:

FreeSurfer version: 7.1.1-centos8_x86_64
Operative System: CentOS8
Hardware: Supercomputer - 68 nodes of Lenovo ThinkSystem 
SD530
Line run for that subject:
recon-all -subjid NoUMA0233 -i filepath.nii -all -qcache -parallel -openmp 16

When opening recon-all.log, it keeps adding the following lines:

Remesher::removeTria( 240873 )
Remesher::removeTria( 240876 )
 NEXTIDX : 88755
 Remesher::removeCollapsedTrias( 88755 , 120326 )
 v_to_t[vidx] :
 Trias are identical : ... removing ...

When opening the error.log of the complete job, there are several lines of this 
error:

rm: No match.

Any advice will be of great help! Thanks a big lot!
Best,
Diana Ortega Cruz.
PhD Student
Laboratory for Clinical Neuroscience
Centro de Tecnología Biomédica - 

[Freesurfer] Labels #601-#628

[A.R. Sekar]

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Hello Experts,

I am trying to isolate ROIs using labels #601-#628 however I am getting the 
following output and it is the same for each label. Any idea what is wrong here?

Thanks for your help!


Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol raparc+aseg.nii 
--outprefix raparc+aseg_labels --L $label 601

Input file: raparc+aseg.nii

Output prefix: raparc+aseg_labels

mri_convert raparc+aseg.nii raparc+aseg.nii.gz

reading from raparc+aseg.nii...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 1, 0)

k_ras = (0, 0, 1)

writing to raparc+aseg.nii.gz...

Label of interest: 601

Number of voxels and volume for label 601 is = (0, 0.00mm^3)

mri_binarize --i raparc+aseg.nii.gz --match 601 --o 
raparc+aseg_labels_label601.mgz

7.1.1

cwd /Users/akilasekar/Desktop/B301001

cmdline mri_binarize --i raparc+aseg.nii.gz --match 601 --o 
raparc+aseg_labels_label601.mgz

sysname  Darwin

hostname Akilas-MacBook-Air.local

machine  x86_64

user akilasekar



input  raparc+aseg.nii.gz

frame  0

nErode3d   0

nErode2d   0

output raparc+aseg_labels_label601.mgz

Binarizing based on matching values

nMatch 1

 0   601

binval1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 0 values in range

Counting number of voxels in first frame

Found -1 voxels in final mask

Count: -1 -1.642760 5242880 -0.19

mri_binarize done

Regards,
Akila
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Re: [Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script

[Eric Deveaud]

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Le 03/06/2021 à 15:53, Eric Deveaud a écrit :
>  External Email - Use Caution
>
> Le 03/06/2021 à 13:46, Eric Deveaud a écrit :
>>   External Email - Use Caution
>>
>> Hello,
>>
>>
>> While installing freesurfer-7.1.1 for centos via rpm
>> (freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem:
>>
>> /usr/local/freesurfer/7.1.1-1/bin/mcparams2reg is a python script that
>> use /usr/bin/env python, not fspython which is 3.6.8
>>
>> either python2 should added as rpm requirement, either mcparams2reg
>> should ported to python3
>
>       same problem with slicedelay
>

     same problem with dsh


     Eric


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Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage with MP2RAGE data

[Corinna Bauer]

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Hi Bruce,
I am just following up on this. Were you able to get mri_normalize to run
on this mp2rage data?

Thanks,

Corinna

On Wed, May 5, 2021 at 6:50 PM Corinna Bauer  wrote:

> Great, thanks. The nu.mgz is attached.
>
> Corinna
>
> On Wed, May 5, 2021 at 6:47 PM Fischl, Bruce 
> wrote:
>
>> H, if you send us the data we will take a look. Just the inputs to
>> mri_normalize should do it for this case
>>
>> Cheers
>>
>> Bruce
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer
>> *Sent:* Wednesday, May 5, 2021 6:45 PM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage
>> with MP2RAGE data
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Bruce,
>>
>>
>>
>> The nu.mgz input into mri_normalize looks ok to me (screenshot attached),
>> as does the talairach registration.
>>
>>
>>
>> Corinna
>>
>>
>>
>> On Wed, May 5, 2021 at 5:39 PM Fischl, Bruce 
>> wrote:
>>
>> Can you take a look at the volume that was the input to mri_normalize and
>> see if it looks ok? And check the talairach
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer
>> *Sent:* Wednesday, May 5, 2021 5:25 PM
>> *To:* Mailing Freesurfer List 
>> *Subject:* [Freesurfer] error at 3d normalization pass 1 of 2 stage with
>> MP2RAGE data
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hello all,
>>
>>
>>
>> I am trying to run recon-all on MP2RAGE data from Philips and it exits
>> with errors at this point:
>>
>> 3d normalization pass 1 of 2
>> error: No such file or directory
>> error: MRInormFindControlPoints: could not find enough control points
>>
>> error: No such file or directory
>> error: MRInormFindControlPoints failed
>> Command exited with non-zero status 253
>>
>>
>>
>> The log file is attached. The input file was the MPRAGE generated on the
>> scanner console (i.e. not the T1 map). I attached a screenshot of orig.mgz
>> viewed in fsleyes. Any thoughts?
>>
>>
>>
>> Thanks!
>>
>>
>>
>> Corinna
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
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>> sender of this message immediately.  Continuing to send or respond to
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[Freesurfer] freesurfer-7.1.1 "" anatomiCutsUtils :: missing lzma python module

[Eric Deveaud]

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Hello,

freesurfer-centos8-7.1.1 rpm installa in singularity container

Singularity> anatomiCutsUtils -h
/usr/local/freesurfer/7.1.1-1/python/packages/pandas/compat/__init__.py:117: 
UserWarning: Could not import the lzma module. Your installed Python is 
incomplete. Attempting to use lzma compression will result in a 
RuntimeError.
   warnings.warn(msg)
Traceback (most recent call last):
   File "/usr/local/freesurfer/7.1.1-1/python/scripts/anatomiCutsUtils", 
line 19, in 
     import graph_tools as gt
ModuleNotFoundError: No module named 'graph_tools'


     regards


     Eric


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Re: [Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script

[Eric Deveaud]

External Email - Use Caution

Le 03/06/2021 à 13:46, Eric Deveaud a écrit :
>  External Email - Use Caution
>
> Hello,
>
>
> While installing freesurfer-7.1.1 for centos via rpm
> (freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem:
>
> /usr/local/freesurfer/7.1.1-1/bin/mcparams2reg is a python script that
> use /usr/bin/env python, not fspython which is 3.6.8
>
> either python2 should added as rpm requirement, either mcparams2reg
> should ported to python3


     same problem with slicedelay


     Eric


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Re: [Freesurfer] freesurfer-7.1.1 :: show_tal ::mri_show: Command not found

[Eric Deveaud]

External Email - Use Caution

Le 03/06/2021 à 14:54, Eric Deveaud a écrit :
>  External Email - Use Caution
>
> Hello freesurfer-7.1.1 installed from rpm on centos8
>
> show_tal tries to call mri_shown a non existing program in
> /usr/local/freesurfer/7.1.1/bin


     tal_compare, same problem


     regards


     Eric


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[Freesurfer] freesurfer-7.1.1 :: rebuild_gca_atlas.csh :: missing subjects.csh

[Eric Deveaud]

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subjects.csh is not installed but rebuild_gca_atlas.csh requires it


     best regards


     Eric


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[Freesurfer] freesurfer-7.1.1 :: show_tal ::mri_show: Command not found

[Eric Deveaud]

External Email - Use Caution

Hello freesurfer-7.1.1 installed from rpm on centos8

show_tal tries to call mri_shown a non existing program in 
/usr/local/freesurfer/7.1.1/bin

     regards

     Eric


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[Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script

[Eric Deveaud]

External Email - Use Caution

Hello,


While installing freesurfer-7.1.1 for centos via rpm 
(freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem:

/usr/local/freesurfer/7.1.1-1/bin/mcparams2reg is a python script that 
use /usr/bin/env python, not fspython which is 3.6.8

either python2 should added as rpm requirement, either mcparams2reg 
should ported to python3


     regards


     Eric



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[Freesurfer] mritotal for talairach registration in FS7

[Gabor Perlaki]

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This email was sent 22 hours ago, but somehow it haven't appeared on the
forum yet. I post it again.

Gabor Perlaki  ezt írta (időpont: 2021. jún. 2.,
Sze, 12:11):

> The default talairach registration is wrong in ~20% of our subjects and
> thus eTIV is also quite inaccurate (e.g. <1000 cc in certain cases). I
> tried -use-mritotal which resulted in much more accurate talairach
> registration.
> My questions:
> Q1, I think it's not a good idea to mix talairach_avi and mritotal
> registrations in a single study, because they can consequently result in
> different eTIV values or initialization parameters affecting the final
> segmentations. Therefore it would be easier to run the whole analysis again
> with mritotal as default rather than correcting the talairach registration
> and rerunning the analysis in separate steps for each subject. Is the
> following command OK for this purpose?
> recon-all -s SUBJ -i input_dicom_file -use-mritotal -all
>
> Q2, Is mritotal only used to calculate talairach.xfm or are there any
> other hidden analysis steps which may perform worse (even though
> talairach.xfm is more accurate) when using it instead of talairach_avi?
>
> Q3, Is it more accurate to use sbTIV instead of eTIV?
>
> Thanks,
> Gabor
>
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