[Freesurfer] mpr2mni305 talaraich transformation error

Hello free surfer developers, I am attempting to compute cortical thickness for anatomical ROIs in neonates, but for some of my subjects I get the following error when I run the auto-recon1 command: \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305

[Freesurfer] Group and ROI analyses in qdec

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 Destrieux atlas. English is not my native

[Freesurfer] Problems transforming T1 to talairach

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 generate the transform matrix, and the segmentation and everything look good. But the T1_in_talairach image

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

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", "covariate 2". What's meaning the sig.nii.gz that it

[Freesurfer] talaraich transformation error

Hello free surfer developers, I am attempting to compute cortical thickness for anatomical ROIs in neonates, but for some of my subjects I get the following error when I run the auto-recon1 command: \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Kyung you should look at the mris_convert help. It has an example of how to convert a scalar overlay like a curv file to ascii: Convert a scalar overlay file to ascii: mris_convert -c lh.thickness lh.white lh.thickness.asc it needs the surface as an input to do the conversion

Re: [Freesurfer] mpr2mni305 talaraich transformation error

Hi Aicha, Have you visually inspected your input image, rawavg.mgz or orig.mgz to make sure they look ok? Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Dijkshoorn, A.B.C. (Aicha)

Re: [Freesurfer] Control Points Not Working

Hi Arsenije, You should never need to add hundreds of control points, just a few dispersed through the problematic area should work. Would you mind uploading your recon to our file drop site and I'll take a look at it? You can send it to my email, ebo...@nmr.mgh.harvard.edu.

Re: [Freesurfer] segmentHA_T2.sh

Hi Eva, I believe this should be fixed in the most recent El Capitan dev version. Let me know if the issue persists. best Andrew On February 1, 2018 at 7:02:19 AM, Iglesias Gonzalez, Eugenio (e.igles...@ucl.ac.uk) wrote: We are looking into all this. We’ll have

Re: [Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

ops. I guess that should have been obvious to me! Thanks! Dorit smime.p7s Description: S/MIME cryptographic signature ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] segmentHA_T2.sh

Dear FS experts, I am now trying the dev version for centos6 to run the segmentHA_T2.sh script. I get the following error: /bin/.: Permission denied. I have tried to change persmissions in freesurfer/bin and still get the same error. Does anyone have experience with this? Best regards,