Re: [Freesurfer] mri_surf2surf help

[Larson, Kathleen E]

External Email - Use Caution

Thanks. I'm now able to run the command without error. However, the surface 
output is not lined up with the original image that I used as the FS input. 
Here is the code I use:

tkregister2 --mov orig.mgz --targ rawavg.mgz --reg register.native.dat --s 
$subject
mri_surf2surf --reg register.native.dat rawavg.mgz --hemi lh --sval-xyz pial 
--tval-xyz rawavg.mgz --tval ./lh.native.pial --s SUBJECT_ID

My guess is that I am somehow not creating the proper transform... do you see 
anything here that I should be doing differently?

Thanks,
Katie

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. 
[dgr...@mgh.harvard.edu]
Sent: Monday, April 08, 2019 12:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_surf2surf help

Have you looked at the help? Run with --help and look at example 4
doug

On 4/4/19 9:56 PM, Larson, Kathleen E wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer developers,
>
> I'm having trouble running the command mri_surf2surf, and I haven't
> been able to find a fix in the message archives (a similar question
> has been asked, but I couldn't find the answer). I am trying to
> convert the pial and white matter surfaces for a series of subjects
> back to the anatomical space. I have computed the registration matrix
> to transform the surfaces, but am having trouble with the
> mri_surf2surf syntax. This is the command I am trying to run:
>
> mri_surf2surf --hemi lh --sval-xyz pial --reg register.native.dat
> rawavg.mgz --tval lh.pial.native --tval-xyz --s 
>
> and I get an error saying that --tval-xyz requires an input volume.
> (The syntax described on the website
> (https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnatdata=02%7C01%7Ckathleen.e.larson%40vanderbilt.edu%7Cba17f3d3fc0c4afcfd3a08d6bc479a23%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636903413085822718sdata=YnDMci9yiERFJr7aODvHk7b91e7cLbUxBRO1agMZAH8%3Dreserved=0)
>  is
> out of date.) I have tried to use rawavg.mgz as the input volume, but
> then I get an output that can only be read as a scalar overlay, and I
> need an actual surface. When I try to use a surface as the input, I
> get an error saying that the file type cannot identified.
>
> Do you have any suggestions for what I am doing wrong?
>
> Thank you,
>
> Kathleen Larson
> Department of Biomedical Engineering
> Vanderbilt University
> 304 Featheringill-Jacobs Hall
> (425)-894-2005
>
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Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

[Greve, Douglas N.,Ph.D.]

Have you looked at the images to verify that there are no major problems 
with it? Can you run it outside of the HCP pipeline to make sure it is 
not an interaction?

On 4/8/19 12:52 PM, Jayasekera, Dinal wrote:
>
> External Email - Use Caution
>
> Dear all,
>
>
> I have been running version 4 of the HCP Pipelines which now used 
> FreeSurfer 6.0. I get the following error when running recon-all using 
> their FreeSurferPipelineBatch script:
>
>
> /nu_evaluate: crashed while running minc_modify_header (termination 
> status=134)/
> /nu_correct: crashed while running nu_evaluate (termination status=65280)/
> /ERROR: nu_correct/
>
> I didn't get this error previously when running FreeSurfer 5.3.0 on 
> the same set of data. Are the MNI tools distributed through FreeSurfer 
> 6.0 sensitive to the operating system and its version? Does anyone 
> have a record of it working on an Ubuntu 14.04 OS?
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
> 2) Platform: Ubuntu 14.04
> 3) recon-all.log: see attached
>
> Kind regards,
>
> *Dinal Jayasekera *
> *
> *
> PhD Candidate | InSITE Fellow 
> Ammar Hawasli Lab 
> Department of Biomedical Engineering 
>  | Washington University in 
> St. Louis 
>
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Re: [Freesurfer] correlation analysis

[Greve, Douglas N.,Ph.D.]

That will compute the average of the Age slope and the NHPT slope. 
Probably not what you want to do

On 4/6/19 12:24 PM, TMS lab wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer team,
>
> I'm running a correlation analysis where I'd like to corelate 
> myelination and a clinical parameter (NHPT) regressing out the effect 
> of age.
>
> My contrast.mtx: 0 0 0.5 0.5
>
> This is my FSGD FILE:
> GroupDescriptorFile 1
> Title Myelin
> Class Main
> Variables Age NHPT
> Inputfs_CGaMain1918.2
> ...
>
> Is the matrix ok?
>
> Thanks
> Rafael
>
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Re: [Freesurfer] The mystery of the missing mcprextreg file

[Greve, Douglas N.,Ph.D.]

Can you verify that that run has the proper number of frames (eg, it 
does not have a single frame)? Did it create fmcpr.mcdat and/or 
mcdat2extreg.log? In the projectdir/log folder, there should be a file 
with a name like /mc-subjectname-bold.log. Can you send that?

On 4/10/19 4:30 PM, Mcnorgan, Christopher wrote:
>
> External Email - Use Caution
>
> Hello, I’ve been trying to get to the bottom of why selxavg3-sess is 
> failing for lack of a mcprextreg motion correction parameters file for 
> one or more of the functional runs.
> I have 6 runs of BOLD data, and following the last failed attempt, we 
> cleared out the run folders to start again from scratch with 
> preprocess on the f.nii volumes.
>
> We are running preproc-sess on a per-run basis:
> preproc-sess -sSUBJECTNAME  -per-run -surface fsaverage lhrh -mni305 -fsd 
> bold-fwhm 4 -sliceorder up  
> After doing this, we find that the folders for runs 1,2,3,4 and 6 
> contain the file mcprextreg, but run 5 does not. Consequently, 
> selxavg3-sess throws an error and aborts when it fails to find this 
> file for run 5. Prior to our do-over, we had the same issue, so it 
> appears that this file is reliably not being generated only for run 5. 
> To further the mystery, a second dataset (different participant) was 
> recently preprocessed and also is missing this file for runs 1 and 5.
>
> I notice that the runs with the missing motion correction parameter 
> each contain a tmpdir.mcdat2extreg.# folder, which suggests that 
> the process might have not completed, though it’s odd that it would 
> have completed for runs 1-4 and 6, but not 5.
>
> I was hoping someone might have some suggestions for debugging why 
> this file might not be getting generated, as well as what steps might 
> be taken to force its creation. I’m going to start by deleting the 
> tmpdir folders.
>
> Thanks,
> Chris
>
> /**
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> * http://ccnlab.buffalo.edu/
> * Office: 716.645.0236
> * Lab: 716.645.0222
> **/
>
>
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[Freesurfer] The mystery of the missing mcprextreg file

[Mcnorgan, Christopher]

External Email - Use Caution

Hello, I’ve been trying to get to the bottom of why selxavg3-sess is failing 
for lack of a mcprextreg motion correction parameters file for one or more of 
the functional runs.
I have 6 runs of BOLD data, and following the last failed attempt, we cleared 
out the run folders to start again from scratch with preprocess on the f.nii 
volumes.

We are running preproc-sess on a per-run basis:

preproc-sess -s SUBJECTNAME -per-run -surface fsaverage lhrh -mni305 -fsd bold 
-fwhm 4 -sliceorder up

After doing this, we find that the folders for runs 1,2,3,4 and 6 contain the 
file mcprextreg, but run 5 does not. Consequently, selxavg3-sess throws an 
error and aborts when it fails to find this file for run 5. Prior to our 
do-over, we had the same issue, so it appears that this file is reliably not 
being generated only for run 5. To further the mystery, a second dataset 
(different participant) was recently preprocessed and also is missing this file 
for runs 1 and 5.

I notice that the runs with the missing motion correction parameter each 
contain a tmpdir.mcdat2extreg.# folder, which suggests that the process 
might have not completed, though it’s odd that it would have completed for runs 
1-4 and 6, but not 5.

I was hoping someone might have some suggestions for debugging why this file 
might not be getting generated, as well as what steps might be taken to force 
its creation. I’m going to start by deleting the tmpdir folders.

Thanks,
Chris

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/

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[Freesurfer] web page library to show freesurfer data (mesh and axial, coronal, sagital slices)

[Gonzalo Rojas Costa]

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Hi:

  Do you know any library to show freesurfer data (mesh and axial,
coronal, sagittal slices) embedded a web page?

  Sincerely,


Gonzalo Rojas Costa

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Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use CautionHi,please, could you suggest colortable for 7 network?Thanks!StefanoIl 27 marzo 2019 alle 16.10 Thomas Yeo  ha scritto:  External Email - Use Caution Hi Stefano,Did you see the colortable that Aihuiping attached? Does it work for you?Thanks,ThomasOn Wed, Mar 27, 2019 at 11:08 PM < std...@virgilio.it> wrote: Please see the attached file.Il 27 marzo 2019 alle 15.39 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:  External Email - Use Caution Hi Stefano,Can you attach your updated colortable, so we can take a look?Thanks,ThomasOn Wed, Mar 27, 2019 at 10:27 PM < std...@virgilio.it> wrote: Yes the left hemisphere is fine.The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt.ThanksStefanoIl 27 marzo 2019 alle 13.09 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:  External Email - Use Caution Hi Stefano,Sorry. Can you confirm left hemisphere is ok? I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114.Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon.  Regards,ThomasOn Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it> wrote: I have renumbered and run:mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txtWhen I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal.What's happened?ThanksBest regards,StefanoIl 26 marzo 2019 alle 13.05 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:  External Email - Use Caution Renumber for visualization purpose. Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit.Thanks, ThomasOn Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote: Thanks.Should I renumber for visualization purpose or for fs-fast?How can I do it?Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:  Hi Stefano,Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while.If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057.Regards,ThomasOn Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote: Hi, my concern is the mri_aparc2aseg command line.In summary, I have done:mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annottkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgzThe output is correct by the color label is those of aparc.Probably the error is the match between the annotations and annot-table.Could you check the command lines, please?ThanksStefanoIl 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < dgr...@mgh.harvard.edu> ha scritto:   Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table  is ok.  On 3/10/19 4:05 PM,  std...@virgilio.it wrote: External Email - Use CautionI will use freeview.Have you any suggestion on the use of fcseed-config option?Are you agree with the command line listed below?fcseed-config -segid ... -seg 

[Freesurfer] Image Analyst Position at the Yale Alzheimer's Disease Research Unit

[Adam Mecca]

External Email - Use Caution

The Yale University Alzheimer’s Disease Research Unit at Yale University
School of Medicine has an opening for a highly qualified and motivated
individual to work on research involving the development of analysis
techniques integrating human imaging data including PET and fMRI for
NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants
must have obtained a Master’s Degree or a Bachelor’s Degree with
significant experience in neuroimaging analysis.

Qualifications:
Strong analytical, and programming skills are essential. Experience in
fMRI, image analysis, algorithm development, and biological applications is
highly desirable. The selected candidate will work under the direction of
Drs. Christopher van Dyck and Adam Mecca.

The successful candidate should have a Master’s Degree or a Bachelor’s
Degree with at least three years of experience in fMRI and/or PET imaging.

Application Instructions:
Interested individuals should email a CV to adam.me...@yale.edu.
Adam Mecca, M.D. Ph.D.
Yale School of Medicine, Department of Psychiatry
Geriatric Psychiatry and the Alzheimer's Disease Research Unit
Tel: (203) 764-8100
Fax: (203) 764-8111
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Re: [Freesurfer] freesurfer longitudinal issue

[Martin Reuter]

Hi Maxime, 

the longitudinal stream aligns images across time. This registration
can (and should) be checked by opening the base/mri/norm.mgz and the
norm.mgz from the tp.long.base (longitudinal) directories. They should
all align. 

Your example looks like you might have openend the images from the
CROSS directories instead of the long? The CROSS time points are in
original space and therefore do not align. Please double check you are
looking at the right files and that the norm.mgz are aligned. 

Best, Martin


On Tue, 2019-03-26 at 13:05 +, maxime GUILLAUME wrote:
> External Email - Use Caution
> Dear freesurfer experts,
>  
> I am performing a longitudinal study (2 time points, 1 year apart) in
> patients with Multiple Sclerosis using freesurfer 6.0.
>  
> After following the tutorial for the CROSS, the BASE (where I only
> performed few manual edits of the surfaces) and the LONG steps, I am
> facing a problem with the results of the longitudinal pipeline:
>  
> If I overlay the final surfaces of the different time points (the
> white and pial surfaces of the LONG step) on the BASE template, there
> are major differences between the two time points (see figure
> attached). This happened only on a subset of my subjects.
> One of our collaborators in this study suggested that this might be
> because the patient was positioned differently in the two time
> points, in particular with respect to the z axis (and indeed the
> major differences between the two surfaces are in the topmost area of
> the brain).
> Does anybody have experienced the same problem? And how can I correct
> for it?
>  
> Thank you in advance for your help.
> 
> (*in the capture surfaces of the first visit are in yellow and in
> green for the second visit)
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