Re: [Freesurfer] A note about the Freesurfer license file

[Angstadt, Mike]

I am getting this same glibc message with Freesurfer 6. Unfortunately I have 
tried twice now to re-register and updated the license file to the new file 
that gets emailed to me, but I am still getting the same error. Any ideas what 
else I can try to troubleshoot this issue?

-Mike

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Z K 

Sent: Friday, February 3, 2017 1:23:04 PM
To: Freesurfer support list
Subject: [Freesurfer] A note about the Freesurfer license file

Hello All,

Users on newer linux distributions who upgrade from Freesurfer version
5.3 to version 6.0 may get the following error message:

--
GNU libc version: 2.17
ERROR: Systems running GNU glibc version greater than 2.15
   require a newly formatted license file (it's free). Please
   download a new one from the following page:
   http://surfer.nmr.mgh.harvard.edu/registration.html
--

This is a known issue, and as the message says, it is resolved by
downloading a newly formatted license file from our registration page:

   http://surfer.nmr.mgh.harvard.edu/registration.html

Simply overwrite the old license file with the newly formatted one.
Sorry for any inconvenience this may have caused.

-The Freesurfer team
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[Freesurfer] [Re] Infant Atlas {Disarmed}

[li ki]

Hi Emma

Thanks for your reply~

As I am not major in neuroscience, maybe it is quite hard for me to label the 
image. But thanks a lot and I will try.

Would you please help me:

  1.  The link you provided mentions a new pipeline for infants. Is it 
integrated with specific infant .gcs atlas file? I am happy as this is what I 
really want.
  2.  I provide a new UNC link 
here(https://www.nitrc.org/projects/pediatricatlas). Can I use these in 
FreeSurfer? But I find it hard to replace the default one.

Thanks for you time again.

Best,

Lemon




Hi Lemon


Please see the mailing list archive here for some guidance (the answer is the 
same for infants): 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56037.html


I couldn't see the UNC link you provided. But the basic steps for creating your 
own atlas are:

-label every voxel of the brain in Freeview (for every subject to be used in 
the atlas)

-run mri_ca_train

-run rebuild_gca_atlas.csh script in $FREESURFER_HOME/bin


Best,

Emma



-

Emma Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging



From: freesurfer-bounces at 
nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
 on behalf of li ki https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
Sent: Wednesday, December 6, 2017 2:41 AM
To: freesurfer at 
nmr.mgh.harvard.edu
Subject: [Freesurfer] Infant Atlas


Hi experts,


We are presently involved in a project for analyzing MRI data of 1-3 year old 
children using FreeSurfer. We cannot find a correct infant atlas. From online 
search, I know that an infant atlas is being developed which will be integrated 
into FreeSurfer in the future. （link

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/
）



Can I know when this will be available? If not soon, is there any other methods 
for us to generate an infant(kid) atlas?



Also I know there are infant atlas from 
UNC(http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases),
  how can I use this atlas in Freesurfer?


Best,

Lemon

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[Freesurfer] IndexError: list index out of range

[Ayushi Shukla]

Hello everyone,

I am trying to run a cortical thickness analysis in QDEC. I have recon-all
and qcache but while trying to run asegstats2table, I keep getting the
error-list index out of range.

asegstats2table --subjects 101 102 103 INSP104 INSP105 INSP107 INSP108
INSP109 112 113 114-S 115-S 116-S 117-S INSP119 INSP120 INSP121 INSP122 123
INSP124 125 126 INSP-127 INSP-129 INSP130 INSPD131 INSPD132 133 INSPD134
136 INSP137 INSP138 INSP139 INSP140 INSP141 INSP143 INSP144 --meas volume
--tablefile Vol_HV_stats.txt

SUBJECTS_DIR : /Applications/freesurfer/subjects

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse

seg = strlst[1] # segmentation id is in the 2nd field

IndexError: list index out of range.


This does not happen when I run the same command for a separate group of
subjects. The recon-all and qcache ran without error. So I was hoping you
could help me resolve this issue.


Warm Regards


Ayushi Shukla

Research Assistant

National Institute of Mental Health and Neurosciences

Bangalore, India
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Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

[Hoopes, Andrew]

Hi M del Mar, I think I’ve found the cause - it’s due to a small bug in 
make_average_surface. I should have a fix for you soon (today or tomorrow).

best,
Andrew

> On Dec 7, 2017, at 3:47 PM, M del Mar Velasco  wrote:
> 
> Hi,
> 
> Have you take a look at our data? Have you find any possible cause? We need 
> to continue with our analysis and it is now stopped.
> 
> Thanks you in advance,
> 
> M del Mar
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Re: [Freesurfer] mri_vol2surf wrong hemisphere

[Defenderfer, Matthew K]

Hi Doug,


FSLView gives a label of L and R and the parcels on the LH in fslview match the 
LH parcels in their included Excel spreadsheet. That's really all the 
verification I have for it right now. It's possible they switched the 
hemispheres when they made the original parcellation volume before making the 
excel sheet, but I don't know how likely that is. Is there anything I can do to 
help out with this?


-Matt


Matthew K. Defenderfer B.S. | Graduate Research Assistant

Graduate Biomedical Sciences | Neuroscience

UAB | The University of Alabama at Birmingham

Laboratory of Kristina Visscher, PhD

Department of Neurobiology

CIRC 111 | C: (865) 805-6389



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

Sent: Monday, December 4, 2017 11:46:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2surf wrong hemisphere

How do you know what is right and left in the volume?


On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote:
>
> Hi,
>
> I have a strange issue I can't figure out. I am currently trying to
> use the parcellation from Gordon et al. 2014
> (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs
> for the frontoparietal network. They provided a volume of the
> parcellation in MNI152 space for public use. I took this volume and
> applied the mri_vol2surf command to it to create 2 overlays of the
> parcels, 1 for each hemisphere. The code was:
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage
> --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage
> --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh
>
> The code ran, but the LH parcels in the volume were transferred to the
> RH on the surface and vice versa. This is a problem since the
> parcellation is not symmetric across hemispheres.This is not a problem
> with the volume either as I looked at it overlayed with the MNI152
> brain in fslview and saw that the parcels were on the correct
> hemisphere. Another problem is that 1 of the frontoparietal parcels,
> number 24, was not found on the surface of either hemisphere after
> turning it to a surface. I don't know why this would be the case since
> there are all cortical parcels.
>
> I have also tried this with a volume ROI that is only located on the
> left hemisphere. After running essentially the same vol2surf command
> as above, the ROI only appeared on the RH surface. I am using
> mri_vol2surf from Freesurfer v6.0.0
>
>
> Any help would be greatly appreciated. Thank you!
>
> Best,
> Matthew Defenderfer
>
>
> *Matthew K. Defenderfer B.S. | Graduate Research Assistant*
>
> Graduate Biomedical Sciences|Neuroscience
>
> UAB | The University of Alabama at Birmingham
>
> Laboratory of Kristina Visscher, PhD
>
> Department of Neurobiology
>
> CIRC 111 | C: (865) 805-6389
>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] PET partial volume correction:mri_gtmpvc error

[Douglas N Greve]

Hi  Elena, it looks like the aseg.mgz has several unexpected segments in 
it. The aseg.auto.mgz looks ok, so I think FS is working properly. It 
looks like you made some changes to the aseg. What did you do?


On 12/06/2017 03:51 PM, Douglas N Greve wrote:
> Did you run this through the standard FS pipeline? If so, can you send
> me the FS analysis for this subject? You can upload it here
>
> https://gate.nmr.mgh.harvard.edu/filedrop2
>
>
> On 12/06/2017 09:46 AM, Herranz Muelas, Elena wrote:
>> Dear Freesurfers,
>>
>>
>> I am trying to apply partial volume correction to my PET images,
>> following  the steps explained in the PetSurfer wiki.
>>
>>
>> When I run the mri_gtmpvc command, it works fine for most of the
>> subjects but for some of them I get the following error message:
>>
>>
>> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space
>> Loading input
>> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz
>>    done loading input 1 frames
>> $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
>> setenv SUBJECTS_DIR
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
>> cd /autofs/space/alicudi_002/users/mscat/users/elena/scripts/PVC
>> mri_gtmpvc --i
>> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz
>> --reg
>> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.reg.lta
>> --psf 6 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx
>> .01 --o
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output
>> sysname  Linux
>> hostname alicudi.nmr.mgh.harvard.edu
>> machine  x86_64
>> user ehmuelas
>> vgthresh   0.001000
>> nReplace   18
>> 0. 0. 0. 0. 0. 0.
>> 40 avail.processors, using 1
>> Creating output directory
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output
>> Loading seg for gtm
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.mgz
>> Loading seg ctab
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.ctab
>> Reading
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.lta
>> Replacing 18
>> Pruning ctab
>> *Checking tissue type
>> ERROR: CheckSegTissueType() tissue type for seg 64 Right-F3orb not set
>> Failed tissue type check
>> *
>>
>>
>> And the command line that I ran:
>>
>> mri_gtmpvc --i $path_to_suvr/SUVR.nii.gz --reg
>> $path_to_suvr/SUVR.reg.lta --psf 6 --seg gtmseg.mgz
>> --default-seg-merge  --auto-mask PSF .01 --mgx .01 --o
>> $path_to_recon/$subj"_recon"/gtmpvc.output
>>
>>
>> Could you please help me out with this?
>>
>>
>> Many thanks in advance!
>>
>>
>> Elena
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] non-brain region

[Boyd, Emma]

Hi Ramesh,


Unless these non-brain regions affect the surfaces then it is fine to leave it 
as is. Your image looks fine to me.

Emma



-

Emma Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ramesh Babu 

Sent: Thursday, December 7, 2017 6:49 AM
To: Freesurfer support list
Subject: [Freesurfer] non-brain region

Dear Experts,

I performed recon-all all precess and it finished without any error. However I 
found some parts of non-brain regions are left over. Should I correct it or I 
can leave it? Please see the attached file and give your suggestions.

Thanks in advance
RB
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[Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess

[Taylor, Johnmark]

Thanks once again for all the help on this. I am running the GLM in native
space, typically so that I can get the beta values to use in an MVPA
analysis. So it sounds like if you specify per-run motion-correction and
registration, and don't tell it to resample to anything (e.g., the MNI
brain or the surface), then there's no guarantee that the voxels will
properly line up if you want to do, for instance, a single-subject GLM in
the subject's native space? So in this case, per-session motion correction
would be better so that all the functional volumes in the session are
registered properly?


> Thank you, this is very helpful! A few quick followup questions:
>
> 1) If you don't specifically tell preproc-sess what space to resample
> too (e.g., by using the "-surface" or "-mni305" flags), does it
> automatically resample to the subject's anatomical volume, then?
I don't think it will do anything if you don't specify
>
> 2) If fmc.nii.gz is already registered to the subject's volume, then
> how come a registration file has to be specified when visualizing GLM
> results using tksurfer? If fmc.nii.gz is already resampled to
> anatomical space, then surely any GLM contrasts should be as well, no?
fmc is not registered to the anatomical, it is registered to the
template. The template is registered to the anat through the
registration file. The data are still in the native functional space.
>
> 3) If per-run motion correction and registration is specified in
> pre-proc sess, then there will be a different functional-->structural
> transformation for each run, correct?
Correct
> If this is the case, then when visualizing session-wide GLM results
> using tksurfer, which registration file should be specified when
> loading up the overlay, since there'll be a different registration
> file for each run?
In what space are you doing the GLM? Usually, the raw data are resampled
onto the surface (eg, fmc.fsaverage.lh.sm05.nii.gz), and the GLM is done
in this spae.so no registration is needed.
>
> Apologies for these (probably basic) questions, I just want to make
> sure I am crystal-clear on what preproc-sess is doing.
>
> Cheers, and many thanks,
>
> JohnMark
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Re: [Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess

[Douglas N Greve]

yes and yes


On 12/07/2017 02:23 PM, Taylor, Johnmark wrote:
> Thanks once again for all the help on this. I am running the GLM in 
> native space, typically so that I can get the beta values to use in an 
> MVPA analysis. So it sounds like if you specify per-run 
> motion-correction and registration, and don't tell it to resample to 
> anything (e.g., the MNI brain or the surface), then there's no 
> guarantee that the voxels will properly line up if you want to do, for 
> instance, a single-subject GLM in the subject's native space? So in 
> this case, per-session motion correction would be better so that all 
> the functional volumes in the session are registered properly?
>
>
> > Thank you, this is very helpful! A few quick followup questions:
> >
> > 1) If you don't specifically tell preproc-sess what space to resample
> > too (e.g., by using the "-surface" or "-mni305" flags), does it
> > automatically resample to the subject's anatomical volume, then?
> I don't think it will do anything if you don't specify
> >
> > 2) If fmc.nii.gz is already registered to the subject's volume, then
> > how come a registration file has to be specified when visualizing GLM
> > results using tksurfer? If fmc.nii.gz is already resampled to
> > anatomical space, then surely any GLM contrasts should be as well, no?
> fmc is not registered to the anatomical, it is registered to the
> template. The template is registered to the anat through the
> registration file. The data are still in the native functional space.
> >
> > 3) If per-run motion correction and registration is specified in
> > pre-proc sess, then there will be a different functional-->structural
> > transformation for each run, correct?
> Correct
> > If this is the case, then when visualizing session-wide GLM results
> > using tksurfer, which registration file should be specified when
> > loading up the overlay, since there'll be a different registration
> > file for each run?
> In what space are you doing the GLM? Usually, the raw data are resampled
> onto the surface (eg, fmc.fsaverage.lh.sm05.nii.gz), and the GLM is done
> in this spae.so no registration is needed.
> >
> > Apologies for these (probably basic) questions, I just want to make
> > sure I am crystal-clear on what preproc-sess is doing.
> >
> > Cheers, and many thanks,
> >
> > JohnMark
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Postdoctoral Scholar in Neuroimaging of Epilepsy and Brain Tumors

[Marshall, Anisa]

Dear all,

We are seeking a full-time postdoctoral scholar to work with a 
multidisciplinary team of scientists on projects related to the use of 
multimodal imaging for improving cognitive and health outcomes in patients with 
epilepsy and brain tumors.

Our team includes full-time faculty from Psychiatry, Radiology, Neurosciences, 
and Radiation Oncology at UC San Diego.   This group of researchers and 
clinical investigators are primarily focused on integrating research imaging 
tools and genetic information into the clinical work flow to directly and 
immediately improve patient outcomes.   The scholar will work closely with 
other postdoctoral fellows, medical residents, graduate students, research 
assistants, and faculty members to help develop methods, analyze structural, 
diffusion, and functional (fMRI) imaging data, prepare manuscripts and assist 
with grant applications.

The fellow should have strong programming and writing skills, experience in 
neuroimaging or a related field, and a strong interest in pursuing an academic 
career path.  Applicants with a strong background in bioengineering, cognitive 
science, and/or experience in machine learning and other multidimensional data 
integration approaches are encouraged to apply.

Location:  UCSD Center for Multimodal Imaging and Genetics (CMIG)
  UCSD  Center for Translational Imaging and Precision Medicine (CTIPM)

Start date:  Flexible, but no later than Spring/Summer 2018

This position is located at the UCSD CMIG, which is located on the East Medical 
Campus in La Jolla, CA in the Altman CTRI.  The fellow will share an office 
with another postdoctoral fellow and have direct access to two 750 GE systems.

Please send application to Dr. Carrie McDonald 
(camcdon...@ucsd.edu).


Kind regards,
Anisa

 --
Anisa Marshall, MS
Neuroimaging Research Associate
Center for Multimodal Imaging and Genetics (CMIG)
UC San Diego

Office phone: (858) 246-0291
a6marsh...@ucsd.edu
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[Freesurfer] [Re] medial wall label in Freesurfer 6

[M del Mar Velasco]

Hi,

Have you take a look at our data? Have you find any possible cause? We need to 
continue with our analysis and it is now stopped.

Thanks you in advance,

M del Mar
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