Re: [Freesurfer] Freesurfer 7T MPRAGE

External Email - Use Caution Dear Manoj, in case you want to rely on tools provided with FreeSurfer only, N3 can produce good results even for 7T data. However, in my experience, you need to supply a brainmask to N3 to achieve very similar results compared to SPM. Otherwise, e

Re: [Freesurfer] Cortical inflation and maintenance of surface voxel intensity

Dear Freesurfer experts, Thank you for the quick response Dr. Greve! It`s an attempt to measure siderosis area, a thin (pathologically), small and blooming cortical signal seen through SWI (due to B0 inhomogeneity). We did: Recon-all SWI BET and registration to T1 #BET bet $SUB

[Freesurfer] pcc.mgh files from mri_glmfit using --pvr

External Email - Use Caution I am running mri_glmfit using the --pvr option and do not get a pcc.mgh file with the output. I found an old thread from 2017 in which Douglas Greve explained that "mri_glmfit will not generate a pcc file with --pvr. I think I just did not get around to

[Freesurfer] Freesurfer 7T MPRAGE

External Email - Use Caution Hi, I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In previous threads, a few people have suggested using SPM to correct for bias first and then running recon-all. Alternatively I saw a thread which suggests modifying the mri_

Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?

External Email - Use Caution Ah okay, I understand now, thank you very much for the help! In hindsight this was a stupid question. What you said makes things perfectly clear. Thanks again! From: Mohammad Rashid <17m...@queensu.ca> Sent: Monday, Jan

Re: [Freesurfer] (no subject)

Are you sure you have permission to view that file? On 1/6/20 5:01 PM, Boris Rauchmann wrote: > External Email - Use Caution > > I’m sure just double checked it. I don’t know what’s wrong here. > > Von meinem iPhone gesendet > >>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. >>

Re: [Freesurfer] (no subject)

External Email - Use Caution I’m sure just double checked it. I don’t know what’s wrong here. Von meinem iPhone gesendet >> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. >> : > This is not making any sense to me. Are you sure you are in > $SUBJECTS_DIR/1122/mri when

[Freesurfer] Recommendation for CFT and CWT FreeSurfer analysis

External Email - Use Caution Hi, I am using Monte-Carlo simulations (for cortical thickness and volume - behavioral analysis) for clusterwise correction for multiple comparisons. My results are either significant at (i) CFT < 0.001 and CWT < 0.1 (i.e., CWT = 0.07) (smoothing 12 m

Re: [Freesurfer] Unable to run recon all

External Email - Use Caution Hi Dough, I just uploaded one of the files on Martinos Center File Drop . I hope that works ! (Somehow, uploading through ftp was taking too long). Thanks. On Mon, Jan 6, 2020 at 11:19 AM Greve, Douglas N.

Re: [Freesurfer] (no subject)

This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder? On 1/3/20 3:07 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for testing it. As be

Re: [Freesurfer] Cortical inflation and maintenance of surface voxel intensity

Hi Pedro, what you are trying to do is certainly possible. It looks like you are doing the right thing as far as I can tell, but I got a little lost after step 4, particularly the "Analyze measured signal" step. One other thing that may be an issue is what projection fraction you used in the mr

Re: [Freesurfer] Unable to run recon all

It is not clear why it failed for these subjects (always happens at the same place). Can you upload one of them for me to take a look at? here are the instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  in

Re: [Freesurfer] Run Recon-all Parallel on Linux

External Email - Use Caution Dear Frank, I have updated the header of the script with much more detailed instructions. I hope they help. If not, let me know where you are stuck. Tim > On January 6, 2020 at 2:56 PM Frank Chau wrote: > > > External Email - Use Caution

Re: [Freesurfer] Run Recon-all Parallel on Linux

External Email - Use Caution Dear Tim, Sorry, I am a Linux code beginner. I installed the GNU parallel in my Linux. May I know how to adapt the script of “ run_reconall_parallel_wrapper.bash” to my own need? Thank you. Regards Frank > On Jan 4, 2020, at 6:12 PM, Tim Schäfer

Re: [Freesurfer] Question regarding T1 map from spoiled 3D GRE

External Email - Use Caution Thanks for the reply, Bruce! I've done some research and found the following publication showing how T1 quantification based on the VIBE sequence can be done offline, however, it doesn't seem to be straightforward as hoped: Rapid T1 quantification from

Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?

External Email - Use Caution In your command line: `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` you run the command only for that single subject, 'subj507'. That is exactly what will happen, no command will be run for the other subjects, so their data remains un