Re: [Freesurfer] Cannot Locate Newly Completed Recon-all Data

External Email - Use Caution Great, thank you for the confirmation! All my best, Joanna -- Joanna Eckhardt Neurosciences Graduate Program University of California, San Diego From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas

Re: [Freesurfer] mri_surf2surf error: could not read surface

It looks like you stopped the job and restarted it. Is that correct? If so, I think something might have gotten out of sync. If you did not make any edits (eg, to correct the defects), then can you start it from scratch? On 5/12/2022 4:29 PM, Margot Wagner wrote: External Email - Use

Re: [Freesurfer] mri_surf2surf error

That mgh file has nothing in it (all dimensions 0). How did you create it? On 5/12/2022 5:20 PM, Zhang, Fan wrote: External Email - Use Caution Hi Dr. Greve, I got this when I ran the line you sent. Thanks, Fan Hans-iMac-Pro:CCn_band fanzhang$ mri_info lh.CCn_band.Seed1_20220314.V1

Re: [Freesurfer] resample_type ignored by mri_convert with --like argument?

Sorry, one more thing. Add --regheader to the command lien On 5/12/2022 5:12 PM, James Hengenius wrote: External Email - Use Caution Hi Douglas, Thanks for the suggestion! However, using mri_vol2vol generates the error message: ERROR: SUBJECTS_DIR undefined. If I set SUBJECTS

Re: [Freesurfer] mri_surf2surf error

External Email - Use Caution Hi Dr. Greve, I got this when I ran the line you sent. Thanks, Fan Hans-iMac-Pro:CCn_band fanzhang$ mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh Volume information for lh.CCn_band.Seed1_20220314.V1.13subjs.mgh type: MGH dimen

Re: [Freesurfer] resample_type ignored by mri_convert with --like argument?

External Email - Use Caution Hi Douglas, Thanks for the suggestion! However, using mri_vol2vol generates the error message: ERROR: SUBJECTS_DIR undefined. > If I set SUBJECTS_DIR to the study directory, I get the following error: movvol ICBM152_2009c_AtlasWhite.nii.gz > targvo

Re: [Freesurfer] [External] Re: [External] Re: Reversing mri_convert

I don't know. You describe a lot of steps which were hard to follow. Without digging into it, I would have a hard time recommending anything. You can always just register your ASL directly to the anatomical (bbregister) and resamploe On 5/12/2022 4:18 PM, Zeng, Victor (BIDMC - Keshavan - Psych

Re: [Freesurfer] [External] Re: [External] Re: Reversing mri_convert

External Email - Use Caution This was part of an independent ASL pipeline called ExploreASL. I do not know 100% the details, but in short the orig.mgz was converted to a .nii through mri_convert for CAT12 and was registered to some native space, the deformation field was saved i

Re: [Freesurfer] Cannot Locate Newly Completed Recon-all Data

You do not need to rerun; it would generate the same result. On 5/12/2022 12:50 PM, Joanna L Eckhardt wrote: External Email - Use Caution Hi Falk, Thank you for your response. I see, that makes sense. I'll use one of those options to make sure my processed data goes into the correct

Re: [Freesurfer] mri_normalize issues, Version 7

First, can you send the full command line and terminal output? Second, what are you trying to do? Are you running this outside of recon-all? If so, why? On 5/11/2022 5:55 PM, Zoe O'Brien-Moran wrote: External Email - Use Caution Hello FreeSurfer developers, I am attempting to run t

Re: [Freesurfer] resample_type ignored by mri_convert with --like argument?

try this mri_vol2vol --targ T1w_MNI.nii.gz  --interp nearest --mov ICBM152_2009c_AtlasWhite.nii.gz   --o WhiteAtlas_resampled.nii.gz On 5/9/2022 11:58 AM, James Hengenius wrote: External Email - Use Caution Hello FS experts, I'm trying to reslice a third-party atlas into the same r

Re: [Freesurfer] [External] Re: Reversing mri_convert

The ASL has a different vox2ras transform. How did you register the ASL to the anatoical? How did you convert the ASL to the anatomical space? On 5/6/2022 4:47 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution /The output for the orig.mgz is: / Volum

Re: [Freesurfer] Recon-all

On 5/5/2022 9:53 PM, krystaly wrote: External Email - Use Caution Dear Freesurfer experts, I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all command as demonstrated on the website (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claimi

Re: [Freesurfer] error estimates in FS total brain volumes

Can you clarify what you mean by margin of error? What are you looking for? On 5/5/2022 6:10 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, What is a reasonable estimate of the error margin in the total brain volume estimates of Freesurfer? Is there a refere

[Freesurfer] Request VM passcode

External Email - Use Caution Hi, I would like to use the VM with FreeSurfer. Could you send me the passcode? Thanks! Regards, Santi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/li

Re: [Freesurfer] Cannot Locate Newly Completed Recon-all Data

External Email - Use Caution Hi Falk, Thank you for your response. I see, that makes sense. I'll use one of those options to make sure my processed data goes into the correct folder from now on. One more follow up question - I located my processed data in the default directory