Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

brain.finalsurfs is fine if you are just rerunning the pial. Edit brainmask if you are starting earlier so all the downstream volumes including brain.finalsurfs will have the dura removed Cheers Bruce > On Feb 7, 2017, at 10:45 PM, 冉倩 wrote: > > > > >

Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc

I'm not sure if "mri_convert *junc.mnc* junk.mgh" was a typo, however, I tried both (junc.mnc, and junk.mnc), and there were errors on both. You're right, I got the same error (using junk.mnc). I'm going to downgrade and see if that helps. On Tue, Feb 7, 2017 at 7:43 PM, Douglas Greve

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

brain.finalsurfs.mgz? not brainmask.mgz? or brain.finalsurfs.mgz for pial surface edit and brainmask for wm surface edit? At 2017-02-08 11:41:40, "Douglas Greve" wrote: You should edit the brain.finalsurfs.mgz to remove the non-brain then run with

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

You should edit the brain.finalsurfs.mgz to remove the non-brain then run with -autorecon-pial On 2/7/17 10:37 PM, 冉倩 wrote: Hi Prof.Douglas Greve, Yes, probematic surface normally existed near supeiror dura ( aroun superior frontal lobe or parietal lobe or central gry area). Just now I

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

Hi Prof.Douglas Greve, Yes, probematic surface normally existed near supeiror dura ( aroun superior frontal lobe or parietal lobe or central gry area). Just now I am confused about the next steps. If I manually erase ( whether I can modfiy control point just like modify wm) the dura on

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

I think Bruce is referring only to the first image. For the second image, it looks like most of the problematic surface is going through the amygdala or hippocampus in which case it does not need to be fixed. On 2/7/17 9:57 PM, Bruce Fischl wrote: oh yes, it's grabbing a bit of dura. If you

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

Hi Bruce, Thanks for your suggestions. If I manually erase ( whether I can modfiy control point just like modify wm) the dura on the brainmask.mgz to correct pial surface. Then I shoud re-run command: recon-all -autorecon2 -autorecon-3 sub01? or just recon-all -autorecon2-pial -autorecon3

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

oh yes, it's grabbing a bit of dura. If you have a 1mm-ish T2 or FLAIR you can use it to automatically correct this type of problem. Or you can erase the dura in those regions on the brainmask.mgz and recreate the pial surface cheers Bruce On Wed, 8 Feb 2017, 冉倩 wrote: Hi Bruce, Thanks

Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc

It may be the version of minc you are using. On our system, we use version 1.5, but it seems to work with 2.2. I don't have access to 2.3. Can you try this mri_convert orig.mgz orig.nii nii2mnc orig.nii junk.mnc mri_convert junc.mnc junk.mgh I'm thinking that the last command will fail On

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

Hi Qian I'm not sure I understand what you think is wrong in the images you included. The first two locations look quite accurate to me, and I'm not positive but I think the third image the locations you circle are amygdala, so not neocortical at all cheers Bruce On Wed, 8 Feb 2017, 冉倩

Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc

Thanks for getting back to me. I ran that command from the $SUBJECTS_DIR/TEST01/mri folder and this is the output: *-rw-rw-r-- 1 root 1590 31M Feb 7 10:14 > ./tmp.mri_nu_correct.mni.30405/nu1.mnc* I do have multiple disks mounted on the server, but they all have more than enough space. The

Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc

not sure what is going wrong here. For some reason mri_convert does not think that the mnc file is a minc file. Can you verify that you did not run out of space on that disk? Can you send the result of ls -l ./tmp.mri_nu_correct.mni.30405/nu1.mnc On 2/7/17 2:59 PM, Muhammad Khan wrote:

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

Hi Qian, things will be a lot easier if you imbed your comments and images in the email. From the text, I can't tell what you want exactly. The first question had to do with skull stripping. It looks like you had to make a manual edit. This is expected sometimes. If it is more than that, what

Re: [Freesurfer] extract area.pial stats

try cd $SUBJECTS_DIR/subject/surf mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial On 2/7/17 4:48 AM, Clara Kühn wrote: > Dear FreeSurfer experts, > > I'm trying to extract a

Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

Hello Juhyoung, I noticed from the recon-all.log files that you are using freesurfer v5.2. It was revealed that this version had issues regarding systematic white surface contraction and placement of the pial surface extending too far:

Re: [Freesurfer] Recon-all - finished with errors

Is that the entire terminal output? On 2/7/17 6:46 AM, Bunday, Karen wrote: > Hi > > Thank you for your email. > > I checked the disk space and there is over 300 GB left. > > I ran the code as you suggested, this is the output: > > "WARNING: # of slices=-92 in header - assuming 124... >

Re: [Freesurfer] recon-all issue {Disarmed}

According to the log file, the error is that you need a new license: GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page:

Re: [Freesurfer] QDEC table .dat

I don't know what you did, but that is still a binary file not a text file On 2/7/17 4:27 PM, Leblanc Élizabel wrote: Hi Freesurfer's expert, I have some trouble with the dec.table.dat file, as many others as I can see. I am using a mac OS x, I took an excel file with my 4 variables and open

Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

Dear Matt, I do not use HCP pipeline scripts for this project. This is standard 1x1x1 mm3 data so I thought standard freeSurfer pipeline could work well here. I also thought that standard recon-all version 6.0 with this data should work better than v5.3 which, I expect, solved some issues

Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

Since I believe you said you are using my code, I would recommend to stick with 5.3 at this time. Peace, Matt. From: on behalf of Antonin Skoch Reply-To: Freesurfer support list Date: Tuesday, February

[Freesurfer] QDEC table .dat

Hi Freesurfer's expert, I have some trouble with the dec.table.dat file, as many others as I can see. I am using a mac OS x, I took an excel file with my 4 variables and open it in a .txt format. then I tried to convert it to a .dat file. I think it worked well (I wrote mv qdec.table.txt

Re: [Freesurfer] -first_wm_peak with -hires in v6.0 (search for peak in second derivative)

if I can find the time! On Tue, 7 Feb 2017, Antonin Skoch wrote: Dear Bruce, Would you recommend to use -first_wm_peak with -hires option? My tests with -first_wm_peak on v6.0 ( with search for peak in second derivative) indicate that the white surface is placed too much internally with

Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

Dear Bruce, thank you for the feedback. I would definitely be interested in 6.1 beta. What is the approximate timeline of release? We are working on quite large project (involving -FLAIRpial) and I have to decide whether to go to v6.0 or to stick with v5.3. Do you think that so far the 5.3

Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

Hi Juhyoung this is a pretty odd bug, but I do have a patch for it. What hardware/software environment are you using? cheers Bruce On Mon, 6 Feb 2017, Juhyoung Ryu wrote: Hi FS developers, I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using

Re: [Freesurfer] (no subject)

Also, what is this "old FreeSurfer 6". Are you referring to a beta? On 02/07/2017 03:24 PM, Iglesias Gonzalez, Eugenio wrote: > Dear Stephen, > I would definitely rerun, for the sake of reproducibility. The results > are sensitive not only to changes in the subfield module (which I > believe I

Re: [Freesurfer] (no subject)

Dear Stephen, I would definitely rerun, for the sake of reproducibility. The results are sensitive not only to changes in the subfield module (which I believe I didn’t modify in between your release and the final 6.0), but also to changes in the main FreeSurfer stream. So, your results are

Re: [Freesurfer] T2 and control points

Thank you very much Antonin. It worked. Best, Paul On Tue, Feb 7, 2017 at 2:36 PM, Antonin Skoch wrote: > Dear Paul, > > I don't know it it solves your problem, but if you are using bash shell, you > have to source SetUpFreeSurfer.sh, not SetUpFreeSurfer.csh. > > And, do you have

[Freesurfer] (no subject)

Dear Dr. Iglesias, Using the originally released version 6 (the one that was "unreleased") I ran the recon -all -all and the subfield segmentations on a sample. I noticed that the program was taken down then put back online after some updates. Do you recommend we re-run these segmentations

Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

Hi Antonin yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We have been optimizing things in the past week for T2/FLAIR and I expect 6.1 will be better for them. We can give you a beta soon if you like. cheers Bruce On Tue, 7 Feb 2017, Antonin Skoch wrote: > Dear

Re: [Freesurfer] T2 and control points

Dear Paul, I don't know it it solves your problem, but if you are using bash shell, you have to source SetUpFreeSurfer.sh, not SetUpFreeSurfer.csh. And, do you have FREESURFER_HOME variable properly set before running the script? To check that, put echo $FREESURFER_HOME to the beginning of

Re: [Freesurfer] T2 and control points

Thanks Antonin and Bruce. Also, I wrote a recon-all script and when I tried to run it, it gave me an error (command not found). Please can anyone help me diagnosis what's wrong with my scripts. I did set my subject directory to the current folder (setenv SUBJECTS_DIR /../folder/; cd

Re: [Freesurfer] recon-all issue {Disarmed}

Yes I’ll attach it here.  I’m using a linux server(Ubuntu). recon-all.log Description: Binary data On Feb 7, 2017, at 12:32 PM, Douglas Greve wrote: Can you send the full recon-all.log? What platform are you running on? On 2/7/17 11:19 AM,

Re: [Freesurfer] recon-all issue

Can you send the full recon-all.log? What platform are you running on? On 2/7/17 11:19 AM, Taylor Hilton wrote: Hi all, Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects. Below is where it has the error in recon-all.log. We also tried running

[Freesurfer] recon-all issue

Hi all, Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects. Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation

Re: [Freesurfer] Percentage of cortex showing significant differences

For fsaverage, the surface area is 74612.58mm2 for lh fsaverage and 73510.21 for rh. These will be listed as "SearchSpace_mm2" in the cluster summary table (if you used mri_glmfit-sim or mri_surfcluster) On 2/6/17 7:09 PM, Bronwyn Overs wrote: Dear mailing list, I have completed a matlab

Re: [Freesurfer] Recon-all - finished with errors

Hi Thank you for your email. I checked the disk space and there is over 300 GB left. I ran the code as you suggested, this is the output: "WARNING: # of slices=-92 in header - assuming 124... Read_signal (/Applications/Freesurfer/subjects/subjKZ/surf/I.001): could not open file No such

[Freesurfer] extract area.pial stats

Dear FreeSurfer experts, I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area: mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f

Re: [Freesurfer] T2 and control points

Dear Paul, maybe this is implicit, but to assure: you have also to include -autorecon3. Therefore the full command is: recon-all -s subject_id -autorecon2-cp -autorecon3 -T2pial Antonin Yes, I think so > On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote: > > Hello, > I ran the