[Freesurfer] Matlab 2016b and localGI

Hi, Hope someone can identify my user error...I've listed below key bits of info (system info, cmdline and error message, echo $PATH, cat .bashrc, cat startup.m). Really appreciate someone taking a look and walking me through a solution to my error? Many Thanks! Jenifer 1) Running

Re: [Freesurfer] Cortical thickness map for a pediatric case

Hi Sneha, I don’t know why this fails. There could be many reasons. Firstmost, the longitudinal stream assumes that head size is constant, which is probably not the case in your data. Looking at the log file however, it seems that recon-all stops in the NU correction step that comes before

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

Sure. Please make sure you have as much as spare disk space as you can. > On Aug 10, 2017, at 4:12 PM, Z Hessam wrote: > > it seems that I should run it again > thank you for your helps > best regards > > On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang

Re: [Freesurfer] mri_surf2vol

Try using mri_label2vol with the ribbon.mgz file. That has a segmenentation of everything inside the white surface. On 08/10/2017 03:58 PM, Rockers, Elijah D. wrote: > I am attempting to create a volume from a surface. My ultimate goal is > to obtain a mask that includes everything "inside"

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

it seems that I should run it again thank you for your helps best regards On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang wrote: > OK. Actually I was wrong, the file has size of 0! I don’t know what > happened when you installed freesurfer or ran recon-all, but the

[Freesurfer] mri_surf2vol

I am attempting to create a volume from a surface. My ultimate goal is to obtain a mask that includes everything "inside" the white matter surfaces. wm.mgz is close, but it would nicer to just get a mask from lh.white and rh.white. I would like these masks to be in the subject's native space.

Re: [Freesurfer] Talairach error

you can visually check it. Also, it is not super critical On 08/10/2017 01:45 PM, Yagmur Ozdemir 19 wrote: > I would prefer to have it run with the tal registration, as I am not entirely > sure if the registration works ok as it was made in another software, but > worst case I will try that

Re: [Freesurfer] Talairach error

I would prefer to have it run with the tal registration, as I am not entirely sure if the registration works ok as it was made in another software, but worst case I will try that option. Thank you! Idil From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Hippocampus subfield segmentation Aborted

Dear Vasudev, I’ve never encountered this problem… Can you please try this? https://uk.mathworks.com/matlabcentral/answers/126994-locale-system-error Cheers, /Eugenio From: on behalf of Dev vasu Reply-To: Freesurfer

Re: [Freesurfer] GLM error - cannot read fsgd file for reading

y.mgh is the input file, usually the output of mris_preproc (after smoothing). See the group analysis tutorial. On 08/10/2017 11:48 AM, Nick Corriveau-Lecavalier wrote: > > Hi Freesurfer team, > > > First, sorry making a new post, I'm having trouble with my email and > I'm not able to reply

Re: [Freesurfer] GLM error - cannot read fsgd file for reading

Hi Freesurfer team, First, sorry making a new post, I'm having trouble with my email and I'm not able to reply directly on my yesterday's post. Here's my issue: I'm trying to make a group analysis with 3 groups using the mri_glmfit command. This it what the terminal says: Loading y from

Re: [Freesurfer] Linear Mixed Effects model

Hi Kasper, your design matrix X should have as many rows as there are measurements. Say if you have m subjects with n measurements each, it will be m*n rows. If different subjects have different numbers of measurements, that's also OK; in such cases the number of rows per subject in X will

Re: [Freesurfer] PET surfer

On 08/10/2017 11:35 AM, John Anderson wrote: > > Dear Dr Greve, > > Thank you very much for the great explanation. I will definitely > correct for PVC using PET surfer. > > Kindly I have one follow-up question and I highly appreciate your input. > > I have PET data for two groups. I studied the

Re: [Freesurfer] PET surfer

Dear Dr Greve, Thank you very much for the great explanation. I will definitely correct for PVC using PET surfer. Kindly I have one follow-up question and I highly appreciate your input. I have PET data for two groups. I studied the difference in PET signal using voxel-wise ( FSL/randomise)

Re: [Freesurfer] Cortical thickness map for a pediatric case

Hi Bruce and Martin, Wanted to follow up and see if you'll got a chance to look at the error and if I could try out something? Thanks, Sneha From: Sneha Pandya Sent: Tuesday, August 8, 2017 11:29:23 AM To: Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] Reporting age differences between groups

I would report it. Just using an age regressor is not guaranteed to remove all age effects. This does not invalidate your study, but it should be mentioned. On 08/09/2017 10:43 PM, Martin Juneja wrote: > Hi, > > I need a general advice from the experts out there. > > I am comparing cortical

[Freesurfer] Hippocampus subfield segmentation Aborted

Dear all, I am encountering following error when i run Hippocampus subfield segmentation "run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266 Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args ". I am annexing the log file for your notice please kindly

Re: [Freesurfer] Hippocampus subfield

Hi Ariel, I second Bruce; we don't have a pipeline to directly measure the subfield thickness. We have, however, tried an indirect volumetric method to compute the thickness (http://nmr.mgh.harvard.edu/~koen/IglesiasNI2014.pdf, the "Experimental setup" section). It requires a (preferably soft)

Re: [Freesurfer] PET surfer

The PET signal can change with a lot of anatomical changes in the brain including thickness, surface area, and gyrification. There is no known regressor that will account for this. Right right way to account for it is with partial volume correction (PVC). It is best to do PVC simultaneously

Re: [Freesurfer] Freesurfer PIB PET image processing

do you mean to run the anatomical analysis on them? No. On 08/10/2017 05:23 AM, M Janani wrote: > Is it correct to process the PiB images using Freesurfer ? > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On

Re: [Freesurfer] Hippocampus subfield

no, not really sorry Bruce On Thu, 10 Aug 2017, Lin, Yizhi wrote: > Dear experts in Freesurfer, > I am doing analysis on hippocampus subfield and I'm wondering if I could > obtain cortical thickness data from each segmentation? Thanks so much! > > Best, > > Ariel > >

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

OK. Actually I was wrong, the file has size of 0! I don’t know what happened when you installed freesurfer or ran recon-all, but the file was not properly written... > On Aug 10, 2017, at 9:34 AM, Z Hessam wrote: > > I copy the *.tar.gz file, and open and install the

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

I copy the *.tar.gz file, and open and install the program by terminal. I am confused because that work last week for this data, but now, this doesn't work. for other datasets, i copy dicom files, then convert them with " recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

How did you put the data on your drive? > On Aug 10, 2017, at 9:25 AM, Z Hessam wrote: > > I didn't copy the file, and drive has 3.7GB free space > > On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang > wrote: >

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

I didn't copy the file, and drive has 3.7GB free space On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang wrote: > Wait, the file size looks too small. Only 1590 bytes. Did the data get > copied properly? Is your drive full? > > On Aug 10, 2017, at 4:40 AM, Z Hessam

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full? > On Aug 10, 2017, at 4:40 AM, Z Hessam wrote: > > it shows: > > -rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 >

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

again that error, it shows: mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

What if you run: freeview -v /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz > On Aug 10, 2017, at 4:40 AM, Z Hessam wrote: > > it shows: > > -rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 >

Re: [Freesurfer] Freesurfer PIB PET image processing

Is it correct to process the PiB images using Freesurfer ? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 10 August 2017 03:41 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

it shows: -rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang wrote: > Hmm, if you run: > > ls -l /media/hessam91/driver2/freesurfer/freesurfer/ >

[Freesurfer] PET surfer

Hi Dr Greve, I have PET data for two groups and I used PET surfer in FSV 6.0 to run the analyses. The pipeline is straightforward and the analysis ran smoothly without any issues. Is it correct procedure to adjust PET signal to differences in gray matter volume or cortical thinness between