[Freesurfer] How to segment subnuclei of thalamus?

Hello Experts, I am interested to do a segmentation of the thalamus subnuclei based on T1 data. Is there any atlas that I could use for this?  Best Wishes, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

[Freesurfer] withdrawing from the mailing list.

Dear Secretariat of Freesurfer mailing list I want to stop receiving emails from the Freesurfer mailing list. Please teach me to withdraw from the mailing list. Sincerely yours. Junji Komatsu in Kanazawa university hospital. ___ Freesurfer mailing li

Re: [Freesurfer] QA Tools v1.2 and future release

Dear Freesurfer Experts, Please excuse my long email yesterday. Now, I finished code update of the outlier detection part for brainstem substructures (bs) and Hippocampal Subfields (hc) modules. Code updated in the similar way as my last email except that I combined the output of both modules to

[Freesurfer] Hippocampal subfield segmentation, file content

Hi All, I have made a hippocampal subfield segmentation using FreeSurfer version 6.0 with multispectral segmentation settings, and have both labels for the right and left hippocampus. The segmentations look very nice when viewed with freeview, so all good. Now, my problem is the file content.

Re: [Freesurfer] Multiple Comparisons Correction thresh error

Hi, We managed to avoid getting the error by typing the following in the terminal before the command: export LC_NUMERIC="en_US.UTF-8" Best,Teodora On Thursday, April 6, 2017, 5:59:05 PM GMT+2, Douglas Greve wrote: I think this is a "language" problem in that it is converting the "1.3" into "1

[Freesurfer] Longitudinal Pipeline

Hi, I wonder if there is a way for mri_robust_template to perform iterative registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years. Thanks, Arman _

Re: [Freesurfer] Hippocampal subfield segmentation, file content

Hi Nina, I’m very glad to hear that the segmentations look satisfactory :-) The ?h.hippoSfLabel.v10.mgz files already have that information; they are label volumes (FreeView assigns colors to the labels for visualization). The lookup table can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt

Re: [Freesurfer] How to segment subnuclei of thalamus?

sorry, not yet. We are working on it Bruce On Fri, 7 Apr 2017, Shane S wrote: Hello Experts, I am interested to do a segmentation of the thalamus subnuclei based on T1 data. Is there any atlas that I could use for this?  Best Wishes, S ___ Freesurf

[Freesurfer] Analyzing xhemi results

Hi free surfers, I have run the xhemi process on the subjects for my study. The study is on stroke patients and their lesions are a mix of left and right hemispheres. In analyzing the results, we want to look at correlations between fmri activation in M1 and the cortical thickness of M1 ipsilesion

Re: [Freesurfer] QDEC and ROI drawing

I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud 2017-04-07 1

Re: [Freesurfer] QDEC and ROI drawing

when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ? On 04/07/2017 11:47 AM, Arnaud Boré wrote: > I used this command line: mri_label2label --srclabel rh.M1_v4.label > --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel > rh.M1_v4.label --regmethod surface --hemi r

Re: [Freesurfer] Analyzing xhemi results

yes, that will work On 04/07/2017 11:11 AM, Marissa Pifer wrote: > Hi free surfers, > > I have run the xhemi process on the subjects for my study. The study > is on stroke patients and their lesions are a mix of left and right > hemispheres. In analyzing the results, we want to look at correlat

Re: [Freesurfer] help

what is your freeview command? Are you trying to view it on a surface? On 04/07/2017 12:53 AM, Dilip Puri wrote: > Hi everyone, > > when I used following command: > > mri_binarize --i myfile.img --match 17 --binval -1 --o > your.lefthippo.nii.gz > > then I got output your.lefthippo.nii.gz file w

[Freesurfer] PETsurfer output error

Hello Freesurfer, I am trying to concat my surface pet file using mris_preproc but I get this error with no output folder or files " mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C

Re: [Freesurfer] PETsurfer output error

It is trying to sample onto fsaverage, but the overlay is already on fsaverage. If you want to use mris_preproc in this way, then the mgx volume needs to be sampled onto the native surface. Since they are already on fsaverage, you can simple run mri_concat C6_01_001_140813/lh.mgx.ctxgm.C601001

Re: [Freesurfer] MRIread (load_nifti)- Out of memory

when they are compressed, a shell command is run to decompress it. When a shell command is run from inside matlab, it creates a "fork". This is a new process identical to the original process, meaning that it takes up twice as much memory. When you decompress it, it does not run the shell scrip

Re: [Freesurfer] Ventricle-to-Brain Ratio

I would use the TVV On 04/06/2017 06:28 PM, Gullickson, James wrote: > Doug, > > Thanks for your reply. > > Difference between the two TVV methods ranges between 1-6% > Difference between the two TBV methods ranges between 2-4% > > Basically, my question is two-fold: > > a) what is the most accur

Re: [Freesurfer] QDEC-Cortical Thickness

You need to select them as categorical variables in the design tab On 04/06/2017 06:01 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: > > Hello Freesurfer Experts, > > I want to compare the cortical thickness between the groups (HC & > Patients), and wanted to know where qdec shows this informatio

Re: [Freesurfer] PETsurfer output error

Thanks doug. Can I include fsgd file in mri_concat or use it during the mri_glmfit stage? Best, Paul On Fri, Apr 7, 2017 at 12:18 PM, Douglas N Greve wrote: > It is trying to sample onto fsaverage, but the overlay is already on > fsaverage. If you want to use mris_preproc in this way, then the m

Re: [Freesurfer] help

I used command freeview -v . then from title bar I uploaded your.lefthippo.nii file. On Fri, Apr 7, 2017 at 9:40 PM, Douglas N Greve wrote: > what is your freeview command? Are you trying to view it on a surface? > > > On 04/07/2017 12:53 AM, Dilip Puri wrote: > > Hi everyone, > > > > when I

Re: [Freesurfer] PETsurfer output error

mri_concat does not take the fsgd file On 04/07/2017 12:25 PM, miracle ozzoude wrote: > Thanks doug. Can I include fsgd file in mri_concat or use it during > the mri_glmfit stage? > Best, > Paul > > On Fri, Apr 7, 2017 at 12:18 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > >

Re: [Freesurfer] help

that freeview command is incorrect. it would need to be something like freeview -v file.nii.gz On 04/07/2017 12:31 PM, Dilip Puri wrote: > I used command > > freeview -v . > > then from title bar I uploaded your.lefthippo.nii file. > > On Fri, Apr 7, 2017 at 9:40 PM, Douglas N Greve > mailto:

Re: [Freesurfer] QDEC and ROI drawing

I try to view it on O_Nap_04MB. I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/

Re: [Freesurfer] PETsurfer output error

Thanks doug. Also, I encountered another error while performing mri_glmfit. Below are the command line, fsgd, matrice and error output. a) mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --fsgd Pet.fsgd dods --C edu.mtx --surf fsaverage lh --cortex --glmdir lh.pet.glmdir b) GroupDescriptorFil

Re: [Freesurfer] PETsurfer output error

you only have two inputs and yet trying to estimate 4 unknowns. You need more subjects On 04/07/2017 01:45 PM, miracle ozzoude wrote: > Thanks doug. Also, I encountered another error while performing > mri_glmfit. Below are the command line, fsgd, matrice and error output. > a) mri_glmfit --y a

Re: [Freesurfer] QDEC and ROI drawing

Do you want me to attach/upload a screenshot of the shift ? 2017-04-07 13:10 GMT-04:00 Arnaud Boré : > I try to view it on O_Nap_04MB. > > I've tried these two command lines: > qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial > --label O_Nap_04MB/label/rh.M1_v4.label > qdec

Re: [Freesurfer] QDEC and ROI drawing

Not yet. Did you try to load it into freeview? If so, do you still see the shift? On 04/07/2017 04:14 PM, Arnaud Boré wrote: > Do you want me to attach/upload a screenshot of the shift ? > > 2017-04-07 13:10 GMT-04:00 Arnaud Boré >: > > I try to view it on O_Na

[Freesurfer] FSurf Webinar Announcement

Dear FreeSurfer Community, The Open Science Grid consortium (http://www.opensciencegrid.org) offers a service “FSurf” which allows large scale batch processing of MRI scans using FreeSurfer. FSurf supports the standard FreeSurfer workflow (autorecon-all) or workflows with arbitrary FreeSurfer op

Re: [Freesurfer] QDEC and ROI drawing

There is no shift in freeview. 2017-04-07 16:35 GMT-04:00 Douglas N Greve : > Not yet. Did you try to load it into freeview? If so, do you still see the > shift? > > > On 04/07/2017 04:14 PM, Arnaud Boré wrote: > >> Do you want me to attach/upload a screenshot of the shift ? >> >> 2017-04-07 13:1

Re: [Freesurfer] correlation coefficient R

Hi Doug, Thank you for your answer! It would be great if you could send me some instructions. Thanks for the help! Douglas N Greve Thu, 06 Apr 2017 13:32:07 -0700