Re: [Freesurfer] meanings of trac-all outputs

External Email - Use Caution Hi Freesurfer experts, Follow up on the last question and correct me if I am wrong, the difference between dlabel/diff/lowb_brain_mask.nii.gz and dmri/nodif_brain_mask.nii.gz is that: > the dlabel/diff/lowb_brain_mask.nii.gz is generated from "bet" (br

Re: [Freesurfer] recon-all error

External Email - Use Caution Dear Yujing, My apologies! Hopefully you can access this now. Kind regards, Rebecca On Tue, Apr 26, 2022 at 11:29 PM Huang, Yujing wrote: > Hi Rebecca, > > > > Thanks for sending the file. But it doesn’t seem that I have the > permission to access

Re: [Freesurfer] Beta values (resubmitting)

External Email - Use Caution Ok. In this case I used the DOSS model (I tested the interaction before and it was not significant). So wouldn't the two groups have the same slope? But the beta values extraction file has only 3 lines (image below). [cid:67fd98ba-4655-445d-bdc7-fd5bbb

[Freesurfer] Resampling of surface-based bivariate data

External Email - Use Caution Is there a way to resample a vertex-by-vertex matrix of data from one subject to another or to ico? For example, I have calculated the Euclidean distance matrix for all the vertices of lh.white for my subjects and wish to find the average distance ma

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

External Email - Use Caution Thank you, Douglas! Is it possible to extract the number of voxels in each segment [of the FreeSurfer DK atlas]? We are hoping to ‘reverse’ the spatial averaging process to get the sum of expression level in each ROI. Thanks, ZZ On Apr 25, 2022, 11:3

Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

Hi Mateo, It looks like mri_convert terminated prematurely when you tried to convert those 512 dicom files. Those error messages are printed when mri_convert wasn’t able to retrieve DTI information from dicom. If you don’t need the DTI values, you can ignore those error messages. Also, lookin

Re: [Freesurfer] Beta values (resubmitting)

3rd line for the slope of CU, 4th line for the slope of CI On 4/25/2022 4:03 PM, Laura Willers de Souza wrote: External Email - Use Caution Thanks so much! I would also like to confirm that I am interpreting the beta values correctly for a second model. Model 2: Two Groups, One Cov

[Freesurfer] Request for 7Zip Archive passcode

External Email - Use Caution Hi, I made a prior request but believe the passcode was sent to someone who posted under my request, and not myself. I just need a passcode to archive the zip folder for file FS_7_2_0_Ubuntu_18_04_06.ova.7z Sorry for the spam! Thank you. _

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

In that case, it mapping the seg into the pet space (see aux/seg.nii.gz) and just averaging over the voxels in each segment. On 4/25/2022 2:34 PM, Zhener Zhang wrote: External Email - Use Caution Hi Douglas, Thanks! We ran the following for one of our subjects: mri_gtmpvc --i sz

Re: [Freesurfer] Cortical depth at each cortical voxel

Hi Panos, Please see my responses interleaved. Best, Iman From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Fotiadis, Panagiotis Sent: Monday, April 25, 2022 10:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical depth at each cortical voxel Hi Iman, Apologies for

Re: [Freesurfer] recon-all error

Hi Rebecca, Thanks for sending the file. But it doesn’t seem that I have the permission to access it. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rebecca Elizabeth Cooper Sent: Monday, April 25, 2022 7:12 PM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all

Re: [Freesurfer] FreeSurfer 7Zip archive passcode

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 25, 2022, at 04:59, Katharina Hense wrote:External Email - Use CautionHello, I'm trying to expand the 7Zip archive for FreeSurfer on the Vi

Re: [Freesurfer] Request for Pass Code VP_7_2_0

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 24, 2022, at 03:25, Kevin Wang wrote:External Email - Use CautionHello,I recently downloaded the archive for the file VP_7_2_0.  Could you please send the pass c

Re: [Freesurfer] pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 23, 2022, at 20:56, Peng, Shichun wrote:External Email - Use CautionCould you please send me the pass code to unzip the file?Thanks,ShichunThe information contai

Re: [Freesurfer] Pass Code

External Email - Use Caution Sending the info to your email shortly. - R.​ On Apr 23, 2022, at 23:43, Activeingredient wrote:External Email - Use CautionHi, can I get the password for FS_7_2_0_ubuntu_18_04_06.ova.7z?Thanks!__

[Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

External Email - Use Caution Hello FreeSurfer Developers I hope i don't spam, if anyone has a clue... I need to convert 512 dicom files from Bruker into .nii . I firstly add .dcm to my Bruker multi gradient echo phase files then enter the following command : mri_convert MRIm