Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Since I'm following the example on the github page, using the ds005 dataset, now with the correct license binding, I am surprised to see freesurfer exiting with errors (but I don't know much about freesurfer): I run this: docker run -ti --rm -v

Re: [Freesurfer] Recon-all -nonuintensitycor

I don't think so On 2/3/18 3:28 PM, Alexis Moscoso wrote: Thanks Douglas. Just one more quick question: will -nonuintensitycor work if I set the -3T flag? As far as I know, -3T changes some parameters of the N3 correction and makes use of Schwarz atlas. I was wondering whether this flag

Re: [Freesurfer] Recon-all -nonuintensitycor

Thanks Douglas. Just one more quick question: will -nonuintensitycor work if I set the -3T flag? As far as I know, -3T changes some parameters of the N3 correction and makes use of Schwarz atlas. I was wondering whether this flag interferes with -nonuintensitycor. El El sáb, 3 feb 2018 a las

Re: [Freesurfer] aparcstat2table with new destrieux atlas

It should be possible. Just specify the annotation you want to use iwth the -p flag (run with -help to get more info) On 1/25/18 12:48 PM, Lisa Delalande wrote: Dear FreeSurfer expert, I would like to use the new destrieux atlas for extracting anatomical data with the aparcstat2table

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Hello Doug, I have uploaded the files you requested. Thank you for your help. Best, Paul On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve wrote: > Can you upload the glmfit folders and the glmfit input (--y file) to our > filedrop? > >

Re: [Freesurfer] FSFAST

That file should be in the same dimensions, no? On 1/30/18 12:19 AM, Ashley Cole wrote: I just noticed that that file "fmc.odd.sm5.nii.gz" is created after selxavg3-sess. I was wondering how can I preprocess the functional image and have the output with the same dimension as the f.nii.gz

Re: [Freesurfer] Recon-all -nonuintensitycor

If you want to just run the recon-all pipeline without using n3, you'll have to do something else. You can copy orig.mgz to nu.mgz (or create a symbolic link, which is probably better), then run with -nonuintensitycor On 1/29/18 7:14 PM, Alexis Moscoso wrote: Hello Freesurfer developers,

Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume mask to the surface space for mri_mcsim using my own template?

You need to map the mask into the fsaverage space. Probably the easiest way to do this is to run recon-all on your template to get surfaces. Then run mri_vol2surf to map your mask onto the surface, then use mris_apply_reg to map your surface mask to fsaverage (make sure to --no-rev since you

Re: [Freesurfer] # voxels above thresholds across aparc+aseg regions - mri_segstats?

Hi Sara, it looks like you are doing a functional constraint. See these slides http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.pptx (tutorial here https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0) and let me know if  you have any questions doug On

Re: [Freesurfer] Misalignment between functional and anatomical data with bbregister

what version of FS are you using? What is your bbregister command line? You should not smooth the data before alignment (usually you would use the template used for MC). You should also make sure that the deobliquing does not mess up the geometry info in the nifti file. Load the template file

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Strange. Can you send me the analysis.info file? On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote: > Hello Dr. Greve, > > Yes it exists. The output below was with debug option. > > Best > Idil > > From: freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] funcroi-table-sess: how to specify frames for multi-band data

Hi Keishi, the frame parameter is the frame in the contrast file. Most of the time this file will only have one frame (-frame 0) unless you have specified a multivariate contrast. This does not have anything to do with multiband. What is your intention when looping through from 0 to 19? doug

Re: [Freesurfer] How to extract stats of the regions that is covered by large clusters

what do you mean by stats? The mean values of the inputs for each cluster and subject will be in the output ("ocd" file). See mri_glmfit-sim --help On 1/31/18 4:48 PM, Shatil, Anwar Shahadat wrote: Hello Experts: After running mri_glmfit sim, I got below clusters: ClusterNo  Max VtxMax  

Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

Can you send the terminal output of one of the runs that fails? On 1/31/18 4:10 PM, Sims, Sara A wrote: Freesurfers, I am trying to use a cortical label to label wm. I am using the following command line: mri_aparc2aseg --s $patient --annot 8V1 –labelwm And most of the time in most

Re: [Freesurfer] Spatial smoothing during preprocessing

On 1/31/18 8:33 PM, Ben Smith wrote: Hi all, I read from the freesurfer discussion archives that when combining FSL FEAT with freesurfer, one should definitely NOT do spatial smoothing in the preprocessing when preparing to examine cortical data.

Re: [Freesurfer] Problems transforming T1 to talairach

Try adding -oc 0 0 0 to the mri_convert command line On 2/2/18 7:27 AM, Helen Beaumont wrote: > I am using the command > mri_convert -at transforms/talairach.xfm brain.mgz brain_in_tal.nii.gz > > to convert a native-space skull-stripped T1 image to talairach space. I used > recon-all to

Re: [Freesurfer] Group and ROI analyses in qdec

On 2/2/18 8:01 AM, Backhausen, Lea wrote: Dear freesurfer experts, I started using qdec for comparing cortical measures in adolescent patients with ADHD versus typically developing adolescents and I have a few questions concerning the ROI analysis as well as the Desikan-Killiany versus

Re: [Freesurfer] One Group (One Factor), Two Covariates

On 2/2/18 7:47 AM, std...@virgilio.it wrote: Hi list, in reference to One Group (One Factor), Two Covariates https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx that has been applied on FS-FAST fcMRI data I obtain three folder, respectively, for "main", "covariate 1",

Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through the mail archives for an example on how to use it On 2/3/18 12:10 PM, std...@virgilio.it wrote: Hi list, Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

Can you upload the glmfit folders and the glmfit input (--y file) to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ On 2/1/18 7:46 PM, miracle ozzoude wrote: Hello Doug, I have attached a screen shot of the mask.mgh for both right and left hemispheres. Everything looks yellow. I

Re: [Freesurfer] White matter hypointensities

Probably just partial volume correction On 2/1/18 3:37 PM, Maksimovskiy, Arkadiy wrote: Dear Experts, I was wondering if anyone might know why the WM hypointensities total number in aseg does not match the sum of left and right white matter hypointensities. Thanks, Arkadiy -- Arkadiy

Re: [Freesurfer] talaraich transformation error

Check and, if necessary, edit the transform.  Then re-run recon-all including the -no-tal-check option On 2/2/18 9:14 AM, Dijkshoorn, A.B.C. (Aicha) wrote: Hello free surfer developers, I am attempting to compute cortical thickness for anatomical ROIs in neonates, but for some of my

[Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

Hi list, Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness? Thanks Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu