Re: [Freesurfer] FS 5.3 and OS X 10.11

Testing freesurfer with the latest version of OSX is ongoing. Ive updated the message to state that "In some cases" freesurfer may fail when running version 5.3 on the lastest version of OSX. The cases where it does fail should be obvious, with an error message is output to the screen. If your

Re: [Freesurfer] Free surfer- correcting for head size

Hi Chistina, the aseg.stats has all that information. You can create a table from all subjects with asegstats2table . It will also contain the ICV (probably called eTIV or something like that). And you can use it in your model, which is probably the best approach. Cheers, Martin On

[Freesurfer] Middle cerebellar peduncle segmentation

Dear experts, I'm trying the brainstem segmentation from Juan Eugenio Iglesias and would like to know if the middle cerebellar peduncle will be added in a near future? Thanks! H. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] pial edits in subject with severe atrophy

Sorry Corinna I meant to answer this the first time but it slipped through the cracks. I doubt there is much you can do if there is that big a lesion. If the topology is wrong and you can't see tissue in those regions it's going to be very hard Bruce On Wed, 10 Feb 2016, Corinna Bauer

[Freesurfer] pial edits in subject with severe atrophy

Dear Experts, I have a subject with severe atrophy in bilateral frontal and parietal regions and after many rounds of edits to the brainmask, wm.mgz, and control points, these regions are still left uncaptured. Is there a way to edit the pial surface to include these grey matter regions? I am

Re: [Freesurfer] error in motion correction

Dear. Freesurfer team. Thanks so much your help and advice. Based on the comments, I'm trying freesurfer version 5.3.0 instead of 4.5.0 now. In our experiment, each participant is scanned twice on different days and the functional scan's brain volume are different (some scans have 33 number of

Re: [Freesurfer] Permission denied error with mri_surfcluster command

I meant for the output files, so the --o in particular On 02/10/2016 01:47 PM, Jennifer Legault wrote: > Douglas, > > Thank you for your quick response. When I add --sd [path_location], I > get the following error: > Loading source values > mri_read(): couldn't determine type of file

Re: [Freesurfer] pial edits in subject with severe atrophy

I should mention that the aseg file captures the GM outside the pial surface. On Wed, Feb 10, 2016 at 1:23 PM, Corinna Bauer wrote: > Thanks, Bruce. > In an earlier thread from '09 with a similar problem ( >

Re: [Freesurfer] error in motion correction

I'm not sure what you are trying to do in the long run. If you have two different scan days and you want to test for differences between them, then analyze each day separately in FSFAST (no problem about the different number of slices). Within a day, each run is separately registered to the

[Freesurfer] comparing multiple runs on the same scan

We would like to confirm that we are getting identical results from multiple freesurfer runs on the same data set. To do so we are comparing identically named files using md5sum and would very much appreciate your thoughts on our results. For multiple files, we concatenate them and pipe the

[Freesurfer] Permission denied error with mri_surfcluster command

Dear experts, I am trying to use the cluster thresholding command for my freesurfer LME outputs as referred to here . Any feedback or comments would be greatly appreciated. I am aware that there have been permission denied

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Douglas, Thank you for your quick response. When I add --sd [path_location], I get the following error: Loading source values mri_read(): couldn't determine type of file [path_location]/rh_time_spval ERROR: could not read rh_time_spval as type Should I use another argument? Best, Jen On

Re: [Freesurfer] error in motion correction

This is the right way to do it, but it may be over kill. I doubt the fMRI results are going to change much whether you use the anatomical from first day only, the 2nd day only, or a combination of the two. On 02/10/2016 01:25 PM, Martin Reuter wrote: > Hi, > > you should co register your

Re: [Freesurfer] pial edits in subject with severe atrophy

ok thanks. On Wed, Feb 10, 2016 at 3:40 PM, Bruce Fischl wrote: > not to my knowledge, but others may have developed something > Bruce > On Wed, 10 Feb > 2016, Corinna Bauer wrote: > > > Thanks, Bruce. > > In an earlier thread from '09 with a similar problem( >

Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

If I use: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon ERROR: Option --fill-ribbon unknown Messaggio originale Da: std...@virgilio.it Data: 8-feb-2016 20.35 A:

Re: [Freesurfer] comparing multiple runs on the same scan

Doug responded to your previous mail with this: Even on the same operating system they will be different because there is stuff in the header that will change. Use mri_diff (volumes, segmentations, and surface overlays) or mris_diff for surfaces to check whether they are different. hth d On

Re: [Freesurfer] comparing multiple runs on the same scan

Thanks very much for getting back so quickly. Please pardon. I’m sure this answer must be in lots of other places. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of dgw Sent: Wednesday, February 10, 2016 3:17 PM To: Freesurfer

Re: [Freesurfer] pial edits in subject with severe atrophy

not to my knowledge, but others may have developed something Bruce On Wed, 10 Feb 2016, Corinna Bauer wrote: > Thanks, Bruce. > In an earlier thread from '09 with a similar > problem(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html > ), it was mentioned that there was

Re: [Freesurfer] comparing multiple runs on the same scan

Hi Don are you saying the 001.mgz is different when created from the same dicom data? Can you run mri_diff on it to see what the difference is? cheers Bruce On Wed, 10 Feb 2016, Krieger, Donald N. wrote: We would like to confirm that we are getting identical results from multiple

Re: [Freesurfer] comparing multiple runs on the same scan

mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are different. In fact, their sizes are slightly different. > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent:

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Thank you very much for your help! I still received a "cannot read file type" error when I only added the path to the output --o part, however when I also added the path to the input file, it worked! I do have one more question: Which argument can I add so that in my output file I see the

Re: [Freesurfer] comparing multiple runs on the same scan

what is the difference in how you created them? On Wed, 10 Feb 2016, Krieger, Donald N. wrote: mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are different. In fact, their sizes are slightly different. -Original Message- From:

Re: [Freesurfer] Middle cerebellar peduncle segmentation

Dear Henri, As of today, there's no plan to add any new labels to the brainstem atlas. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Henri Pazro"

Re: [Freesurfer] pial edits in subject with severe atrophy

Thanks, Bruce. In an earlier thread from '09 with a similar problem ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html), it was mentioned that there was a method being developed to edit the surface mesh. Is that option still available and would it help? Since this step in

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Try specifying the full path to the output On 02/10/2016 12:59 PM, Jennifer Legault wrote: > Dear experts, > > I am trying to use the cluster thresholding command for my freesurfer > LME outputs as referred to here > . > Any

[Freesurfer] difference in 001.mgz found

These runs were executed on the Open Science Grid. So the data file, the scan, was uploaded to grid worker machine, placed in a transitory directory, and processed. The full pathname of the file is included in 001.mgz. I got it by: zcat mri/orig/001.mgz | strings Here are the input and output

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

what is your command line? I think there is a rescaling in which it expcts the phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) scanner. Could that be the problem? On 2/10/16 10:40 PM, Joseph Dien wrote: I ran into the same issue: FSLVersion 5.0.4 FSLVerMaj 5 FSL

Re: [Freesurfer] Processing of young children using Freesurfer

Hi, did you find a hint why my installation of freesurfer is not processing the data at that stage ? It seems to be a general problem, we tried also with other data sets of elder people etc .. Any help appreciated. Yours Frank PD Dr. Frank Zoellner Group Leader "MRI and

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

I ran into the same issue: FSLVersion 5.0.4 FSLVerMaj 5 FSL Version is 5.0.4, must be 3.X or 4.X I downloaded the epidewarp.fsl script from the suggested ftp site and replaced the existing script. It did indeed fix the version incompatibility with FSL 5.x. I ran into a new problem where it

Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

I may have gotten the exact form of the flag wrong. When it says an option is not known, you should try running the command with --help to see if something similar is there. In this way, you might be able to figure it out for yourself rather than have to wait a day or so for us to respond.

Re: [Freesurfer] Permission denied error with mri_surfcluster command

There is a (very long) command line on that page. Mainly you need a csd file. To get that you need the FWHM of your analysis, the voxel-wise threshold, and the sign of the contrast (or abs). Then the relevant output will be the --sum. You can run it with --help to get more info. On 2/10/16

Re: [Freesurfer] abnormal inflated surface

Hi Jasmin, nothing looks wrong with the inflated brain images to me. Remember, the inflated brain doesn't have the same space as the T1 or white matter surface, so they are just centered. And overlap one another as the slice views showed. I'm afraid I can't help with the hippocampal question,

Re: [Freesurfer] abnormal inflated surface

Hello, Thank you for the speedy reply. I ran recon-all and the process occurred without error. I have quality checked the various steps and have found no issues. But this participant's hippocampal volume is approximately 2000 while all the others in my cohort are about 4000. Is it possible for

Re: [Freesurfer] comparing multiple runs on the same scan

It looks like they do give the same results. I have to write something to go through everything systematically which I may not get to till tomorrow. Also I am checking to see whether there was some difference in how 001.mgz was created. The source image file on which we are running freesurfer is

Re: [Freesurfer] comparing multiple runs on the same scan

That probably means that there is something in the header that is different. It should print a report to the terminal. Do they not give the same results? On 02/10/2016 04:36 PM, Krieger, Donald N. wrote: > mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are >

Re: [Freesurfer] difference in 001.mgz found

yes, we store the command lines used to generate a .mgz in the header, so that makes sense Bruce On Thu, 11 Feb 2016, Krieger, Donald N. wrote: These runs were executed on the Open Science Grid. So the data file, the scan, was uploaded to grid worker machine, placed in a transitory directory,

Re: [Freesurfer] difference in 001.mgz found

Thanks for the confirmation, Bruce. I've looked at the other files I spot checked which failed to match. A bunch of the files in directory surf contain a line at the top like "Created by nobody on Mon Feb 8 15:13:58 2016" The mri/transforms/talairach.m3z.inv.?.mgz files contain the pathname of a