Re: [Freesurfer] Recon-all -hires

Dear Bruce, Thanks for your tip. Actually, it didn't work for me. I went to ask one of my colleagues, Martin Reuter, for help, and it turns out that the permission of my files in the $FREESURFER_HOME/bin folder have been changed to 'read only'. Martin helped me to change the files in the

Re: [Freesurfer] GPU compile cuda8/centos7

On 27 November 2017 at 11:02, Meij, Henk wrote: > Just wanted to report back a success. I had to do some fixes so hope this > helps anybody. > > My gpus are GTX1080Ti and the CPU involved is E5-2620 dual 10 core on this > server. > > The vanilla cpu recon-all finished in 7

[Freesurfer] Estimated ICV much lower than mask volume?

Hi experts! We are doing some QA exams with one subject scanned on different 3T scanners (with comparable/nearly identical imaging parameters). Afterwards, we looked into aseg values to compare them with the standard recon-all procedure. And we came across a strange result. Between two scanners

[Freesurfer] Surface-based kernel operations

Dear Freesurfer experts, I would like to preform several operations in surface files using spatial kernels (i.e mean value in a 3x3 grid, nearest neighbour value, etc). In summary, perform operations in the surface such as a 2D matrix/image. Is it possible to do it with Freesurfer? I tried to

[Freesurfer] the ordering in ascii txt file

Dear Freesurfer experts, I used the following mri_convert command to extract the skull stripped image and save it to a txt file. The file contains only one column, and has 256*256*256=16,777,216 rows. Does anybody know the ordering in which 256*256*256 array is transformed to the vector (eg,

Re: [Freesurfer] ERROR: fast_sexavg3() failed\n

Hi experts, I am not sure if my log files are reaching you. I tried sending them twice by now. Could you please let me know if I can send files through here? Thank you very much. Christina > On Nov 15, 2017, at 2:46 PM, Douglas N Greve > wrote: > > Can you

Re: [Freesurfer] MacOS Sierra 10.12.5 dyld lazy symbol binding error

Hi Andrew, That fixed it! Thank you! Best, Kelly On Tue, Nov 28, 2017 at 11:17 AM, Hoopes, Andrew wrote: > Hi Kelly, > > This might have to do with SIP being enabled, which blocks libraries > stored in /usr. I would suggest disabling SIP and rerunning to see if that

Re: [Freesurfer] medial wall label in Freesurfer 6

Hi Sofia, Another user seems to be experiencing a similar issue right now. How many subjects are you trying to average? I haven’t been able to replicate this, so it might require uploading some subjects. Can you send the make_average_volume.log? best, Andrew On Nov 27, 2017, at 10:16 AM,

Re: [Freesurfer] MacOS Sierra 10.12.5 dyld lazy symbol binding error

Hi Kelly, This might have to do with SIP being enabled, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, Andrew On Nov 27, 2017, at 6:33

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi, User M del Mar and me belong to same investigation group, so the problem is common. We have 116 subjects and we detected this trouble. However, we tried to repeat the make_average_subject command using a subgroup (only 60 subjects) and label files were correctly created. Maybe, number of

Re: [Freesurfer] Surface-based kernel operations

Hi Victor the order of vertices/faces is somewhat arbirtry. If you want to write out a convolution I would do it on the sphere (and account for the metric tensor of the chart functions), or flatten and do it in the plane. cheers Bruce On Tue, 28 Nov 2017, Victor Montal Blancafort wrote: >

Re: [Freesurfer] neonatal brain

Hi Aicha, > Thank you for your quick response. Since I am new to freesurfer I have still > a few questions... Thank you in advance for your time! > > Where can I read more about building my own template? On our wiki page there are several pages describing how to build the type of templates

[Freesurfer] Tracula / 0 slices processed in Bedpostx before queuing post processing stage

Hi, I’m having difficulty making BedpostX work on non-tutorial data per the tutorial located here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula The preprocessing has worked without errors, but now

Re: [Freesurfer] Merging two groups

Hi Ramesh probably easiest to symlink them cheers Bruce On Tue, 28 Nov 2017, Ramesh Babu wrote: Hi, I have done recon-all -all processing for 2 groups in separate subjects directories. I want to put all subjects in one dkirectory. Should I copy paste all subject’s folders in one directory

Re: [Freesurfer] Recon-all -hires

I'm glad to hear it worked out Bruce On Tue, 28 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your tip. Actually, it didn't work for me. I went to ask one of my colleagues, Martin Reuter, for help, and it turns out that the permission of my files in the $FREESURFER_HOME/bin folder

Re: [Freesurfer] covariates in Qdec

you need to check age and sex On 11/28/17 3:46 AM, 박경일 wrote: Dear experts, I am trying to compare 2 groups with 2 covariates (age, sex) using qdec. After loading data, design tab displays "diagnosis" in discrete, "age" and "sex" in both continuous (covariates) and nuisance factor boxes.

Re: [Freesurfer] Merging two groups

Thank you very much for your reply. On Mon, Nov 27, 2017 at 10:51 PM, Douglas N Greve wrote: > An easy solution is just to use a symbolic link (the ln command under > linux). That way you don't have to move anything at all. If you want to > move things, I would copy

Re: [Freesurfer] GPU compile cuda8/centos7

Hi, Has all of the GPU code also been updated in the new FS6.0 version or the code is still from the old 5.x but can be compiled with new cuda toolkits? Best regards, -- Shahid. On Mon, Nov 27, 2017 at 9:29 PM, Meij, Henk wrote: > Well, it looks the *_cuda files for

Re: [Freesurfer] Estimated ICV much lower than mask volume?

Hi Patrycja did you check to see if the talairach transform was reasonably accurate? cheers Bruce On Tue, 28 Nov 2017, Patrycja Naumczyk wrote: Hi experts! We are doing some QA exams with one subject scanned on different 3T scanners (with comparable/nearly identical imaging parameters).

[Freesurfer] QDEC and comparing two conditions

Hi FreeSurfer experts, We calculated the correlation between thickness two different behavioral conditions using QDEC. We now want to compare the spatial overlap and difference in thickness-correlation between the two behavioral conditions. We would like to do this both visually as well as

Re: [Freesurfer] the ordering in ascii txt file

Run mri_info and see the Orientation  string. Eg, LIA On 11/28/2017 11:47 AM, Yi Li wrote: > > Dear Freesurfer experts, > > I used the following mri_convert command to extract the skull stripped > image and save it to a txt file. The file contains only one column, > and has

Re: [Freesurfer] Surface-based kernel operations

read_surf.m will read in a surface including the nearest neighbors. the vertices are not ordered in an ordered way On 11/28/2017 11:38 AM, Victor Montal Blancafort wrote: > Dear Freesurfer experts, > > I would like to preform several operations in surface files using > spatial kernels (i.e

[Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

Hi Freesurfer Experts, I've been looking to extract the timecourses of a couple regions of interest from fMRI data that's be registered against anatomical data. I've used commands such as recon-all and preproc-sess on all subjects. I've already used command fcseed-sess to extract timecourses

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

You will need to create a segmentation volume in the subject/mri folder. For BA6, you can use lh.BA6_exvivo.thresh.label to create this volume. Use mri_label2vol. Run it with --help to get examples. You can use example #4 just with the single label above (for the output use a mgz file instead

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

Hi Freesurfer Experts, Can I extract time courses for regions without labels in the subject/mri folder? Thank you for your insight! Best, Jessica On Tue, Nov 28, 2017 at 5:51 PM, Douglas N Greve wrote: > You will need to create a segmentation volume in the

Re: [Freesurfer] GPU compile cuda8/centos7

On 28 November 2017 at 09:12, Dr. M. Shahid wrote: > Has all of the GPU code also been updated in the new FS6.0 version or the > code is still from the old 5.x but can be compiled with new cuda toolkits? I made a small tweak for GCAMorph (primarily ca_register) which

[Freesurfer] covariates in Qdec

Dear experts, I am trying to compare 2 groups with 2 covariates (age, sex) using qdec. After loading data, design tab displays "diagnosis" in discrete, "age" and "sex" in both continuous (covariates) and nuisance factor boxes. I just selected "diagnosis" and click "analyze". Is this a right way