[Freesurfer] smoothing

Dear freesufers, I quick question about smoothing of data in cortical thickness analysis. I have a comparison that is rather borderline significant. When using smoothing of 10 mm I get a limited region in the frontal lobe that is differs between groups. Changing to 15 mm I get larger regions -

Re: [Freesurfer] smoothing

Hi Eric the optimal smoothing kernel more or less matches the size of the effect, so it's impossible to say a priori. A bigger kernel is better if there is more widespread subtle thinning cheers Bruce On Mon, 27 Jul 2015, Erik Lindberg wrote: Dear freesufers, I quick question about

Re: [Freesurfer] QA measures mgz

I can't recommend anything in that case, since I am just relying on available, but very scanty documentation. I think people were using norm.mgz, but the question how these results corespond to other volumes has not been addressed yet. Some normative, semi-technical paper on QA measures in

Re: [Freesurfer] QA measures mgz

it depends on which gm you are looking at. For cortex you can use the brain.mgz, for any subcortical structure you can use the norm cheers Bruce On Mon, 27 Jul 2015, Jacek Manko wrote: I can't recommend anything in that case, since I am just relying on available, but very scanty

Re: [Freesurfer] Recon-all error

hmmm, that usually means you ran out of memory, which is surprising given that that step doesn't take very much. Were there other jobs running on the same machine? On Mon, 27 Jul 2015, Park, Jung Mi wrote: Hello Freesurfer expert I got an error message while running recon-all.   1) subject

[Freesurfer] Recon-all error

Hello Freesurfer expert I got an error message while running recon-all. 1) subject name gencess SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /autofs/cluster/catanagp/users/jumi/subjects/anat/AD0401AG/anat/scripts setenv SUBJECTS_DIR /space/sake/3/users/inverse/subjects cd

Re: [Freesurfer] cluster_wise correction

How did you do the FC analysis? In the volume or on the surface? doug On 07/23/2015 11:00 AM, Meiling Li wrote: Hello Freesurfer Experts I am emailing to ask aome questions about cluster_wise correction on surf. I hope some experts here could help me... The seed_based functional connectivity

Re: [Freesurfer] percent signal change

I think you'll need to contact the FSL list to ask how to convert the COPE volume to a voxel-wise percent signal change. Once you have that, then you can just project that data onto the surface instead of the original COPE. doug On 07/24/2015 05:11 PM, Mariam Sood wrote: Dear Doug, Thank

Re: [Freesurfer] unpack error

Can you send the full command line and full terminal output? doug On 07/25/2015 02:43 PM, Park, Jung Mi wrote: Hi Freesurfer team I did unpacksdcmdir successfully before at Martinos center. Recently I got error message while I was trying to unpacksdcmdir. ; Cannot open

Re: [Freesurfer] [FreeSurfer] multicore recons

thanks i was not using the -open x , correctly On Fri, Jul 24, 2015 at 7:37 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Yes. That is correct. On Jul 24, 2015, at 7:06 PM, joseph veliz josephveli...@gmail.com wrote: so I should run one subject per 4 cores by using -openmp 4 for each of the

Re: [Freesurfer] bad registration using mri_vol2vol

In tkmedit on fsaverage? I just ran something similar (using your /lh.amyg.faceaw.5.3CRFH.anatconstr.p05.n65.label) and it seemed to give the correct results. I viewed it with tkmedit -f /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz -aux dougvolume.nii.gz -ov

Re: [Freesurfer] smoothing

I don't think there is a way to know. for perfect data, the false positive control should be appropriate across all smoothing levels. As you smooth more and more, you can start getting low frequency junk, but this often creeps into the estimation of the FWHM and hurts you more than helps you.

Re: [Freesurfer] Regarding: 3 groups and 1 covariate contrast

The the CAG is a nuisance variable and you are interested in testing for the differnces in thickness with CAG regressed out, then you should do a two step procedure. First run with DODS and test for differences between groups in CAG. This is the contrast you will need: 0 0 0 1 -1 0 0 0 0 1 0

Re: [Freesurfer] pial surface from one hemisphere is crossing the surface of other hemishpere

I have also come across this output. On Fri, Jul 24, 2015 at 6:57 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Antonin not sure - if you upload the subject I'll take a look Bruce On Fri, 24 Jul 2015, Antonin Skoch wrote: Dear experts, I came several times across the

Re: [Freesurfer] Using ROIs in SPM

What are the two T1 images? The command line below will take a label in 152 space and transfer it to mni305 space. I'm not sure what you are actually trying to achieve. doug On 07/23/2015 10:44 AM, amirhossein manzouri wrote: Hi, I found group differences based on T1 images with 8 channel

Re: [Freesurfer] qdec problem

Sorry, I'm having a problem understanding your question. Can you elaborate? doug On 07/27/2015 04:32 AM, marco.m...@tin.it wrote: Hi, I'm Marco from Italy, I've problem with qdec because qdec produces these files in the stats_table directory. How you can see there aren't all those

[Freesurfer] slice timing correction in preproc-sess

Hi list, preproc-sess -s Sess101 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-runproduces fmc file but fmcstc and fmcstcsm are lacking.A- The slice timing correction is performed with the command reported above? Or I should add to command line -stc (furthemore, where I should put it?

Re: [Freesurfer] slice timing correction in preproc-sess

See preproc-sess -help On 07/27/2015 02:30 PM, std...@virgilio.it wrote: Hi list, preproc-sess -s Sess101 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-run produces fmc file but fmcstc and fmcstcsm are lacking. A- The slice timing correction is performed with the command reported

Re: [Freesurfer] Huge difference ini area for the same subject

Hi Doug, Yes, one set of subjects by two editors and no difference in thickness but huge difference on the area between two sets. Actually I want to see f there is any difference between editors for the same set of subjects. On Monday, July 27, 2015, Douglas N Greve gr...@nmr.mgh.harvard.edu

[Freesurfer] recon-all error_cannot find or read transforms/talairach.m3z

Hello Freesurfer expert Running recon-all abruptly stopped with this error message at NMR center; mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR:

Re: [Freesurfer] recon-all error_cannot find or read transforms/talairach.m3z

there is probably an error before that. Can you send the entire recon-all.log? On Mon, 27 Jul 2015, Park, Jung Mi wrote: Hello Freesurfer expert Running recon-all abruptly stopped with this error message at NMR center;  mri_ca_register -invert-and-save transforms/talairach.m3z  Loading,

[Freesurfer] Fafast and matlab question

Dear all,   I loaded the t.nii under a contrast directory in freeview, and then loaded the t.nii to matlab using MRIread.  When I checked the t value for a point, such as 32, 38, 32, the value is 3.96.  Then I got value from the same point (32, 38, 32) in matlab,  I got a different t value.  I

[Freesurfer] (no subject)

Hello Freesurfer Experts, For a longitudinal dataset we worked on some time ago, in version 5.1, we want to add subjects with only one time point. According to the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing we can do this by passing only a single time

[Freesurfer] tkregister2_cmdl

Hi, I’m running FS6 and everything seems to be running fine except that a txt file filled with this error message is created: rm: No match. tkregister2_cmdl: Command not found. tkregister2_cmdl: Command not found. tkregister2_cmdl: Command not found. tkregister2_cmdl: Command not found.

[Freesurfer] Repost: Dividing Entire Scan By Intensity Factor Create Overlay Surface

(I just wanted to follow-up on this request. If it is not possible to do these things, that would also be helpful to know so that I don’t continue to attempt different variations of the options. If any more information is required to make the questions clearer, please let me know what you need

[Freesurfer] qdec problem

Hi, I'm Marco from Italy, I've problem with qdec because qdec produces these files in the stats_table directory. How you can see there aren't all those 'lh.aparc.a2009s' type.Can you help me?Thanks!