[Freesurfer] AD cortical thickness signature

Dear FS experts I’m wondering whether there are ways of getting the single value of ROIs. I mean to get the value of cortical thickness of AD signature areas, such as supra marginal gyrus, inferior frontal cortex.. and so on .. the values of some areas can be get using aparcstats2table (in

[Freesurfer] Recon-all error

Dear mailing list, I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache But for each image the process exits with the following errors: --- #@# 1/1 ID_001 Wed Aug 16 11:39:12

[Freesurfer] FS-FAST outputs is X.mat used? {Disarmed}

Dear all, I have a question regarding the output from selxavg3-sess. I noticed that within an analysis there is a X.mat that looks like a design matrix -- however is this used at any stage of the analysis? The help message in selxavg3-sess reads: "This program will construct the design matrix

Re: [Freesurfer] T1 motion and average

you wouldn't use -rms for the second round. That's a lot of averages though. Is your data quite hires? For 1mm or so we don't usually need more than a single scan at e.g. 3T and 32 channels. If your data is higher than 1mm, you should include the -noconform switch cheers Bruce On Tue, 15

Re: [Freesurfer] T1 motion and average

Dear Dr Bruce, Thank you very much for the quick response mri_average -rms will average the 4 volumes for each MEMPRAGE and output one T1 image. The results is four T1 images. How can I average these four T1 images. Can I merge them and use mri_average -rms gain? Original Message

Re: [Freesurfer] T1 motion and average

Hi John sure, mri_average -rms will take the square root of the sum of squares of the 4 echoes if you want. You could then average them across the MEMPRAGEs if you want cheers Bruce On Tue, 15 Aug 2017, John Anderson wrote: Dear Freesurfer experts, I have noisy four MEMPRAGE images each

Re: [Freesurfer] Help with hippocampal subfield alignment

HI Elizabeth that should definitely not happen. Something must have gone pretty dramatically wrong. If you upload the subject I'll take a look cheers Bruce On Tue, 15 Aug 2017, Elizabeth Hall wrote: Hi Eugenio, It looks like the segmentation is missing all of the left hippocampus in the

Re: [Freesurfer] error in recon-all

hmmm, not sure. Your surface is very big with lots of defects and that is also a very big defect. Can you bring up the lh.inflated.nofix and see if anything is dramatically wrong with it (e.g. cerebellum or skull attached). cheers Bruce On Tue, 15 Aug 2017, 王康程 wrote: Hello FreeSurfer

[Freesurfer] T1 motion and average

Dear Freesurfer experts, I have noisy four MEMPRAGE images each one has four volumes for the same participant. These T1 images were acquired at the same scanning session. I have two question: 1. Is there any tool in free surfer to average these images. 2. Is the average the images a good idea

Re: [Freesurfer] Help with hippocampal subfield alignment

Dear Elizabeth, I would guess that something went seriously wrong in the recon-all with your data. Does Talairach registration and skull strip look reasonable? Antonin Skoch ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Help with hippocampal subfield alignment

Dear Elizabeth, You would have to manually edit the segmentations in both wmparc.mgz and aseg.mgz, which I wouldn’t recommend. Maybe Bruce or Doug have some ideas on how to improve the automated segmentation? Cheers, /Eugenio From: on behalf of Elizabeth

Re: [Freesurfer] Help with hippocampal subfield alignment

Dear Elizabeth, This is pretty unusual. Would you mind taking a look at aseg.mgz? Does the segmentation of the (whole) left hippocampus look fine in ASEG? Cheers, /Eugenio From: on behalf of Elizabeth Hall Reply-To: Freesurfer

[Freesurfer] Help with hippocampal subfield alignment

Hello FreeSurfer Developers, I have run the hippocampal-subfields-T1 tag on a MP2RAGE scan for one of my subjects and find that the subfield segmentation for the left hemisphere only is off (pictures attached). No errors were reported in the log. Is there a way to manually reset the alignment

[Freesurfer] freeview problem on Linux RHEL 7-4 libGLU.so.1

Hello all, I installed the latest version for Linux I get this message when trying to run an example: "freeview.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory" I installed the missing library and now it is in

[Freesurfer] Fwd: Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed} {Disarmed} {Disarmed}

FYI Forwarded Message Subject: Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed} Date: Tue, 15 Aug 2017 09:44:19 -0500 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] use manually defined talairach.xfm

Dear Clemens, this is very strange, since the talairach.xfm is not by default overwritten in recon-all (unless you specified -clean-tal to recon-all). When you rerun your recon-all after modifying talairach.xfm, your automatic talairach registration will be saved into talairach.auto.xfm,

[Freesurfer] (no subject)

Hello, I try to map the surface to the native space, using the following command adjusted for my data: mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname the output is: ERROR: --tval-xyz flag needs 1 argument FYI:

Re: [Freesurfer] SPC in surface area

What is the unit of the spc, which you extract? Fx. in my data I have a -0.49 = does that mean a -0.49 % decrease? BW Kasper Fra: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Martin Reuter Sendt: 19. juli 2017 11:37 Til: Freesurfer support

[Freesurfer] use manually defined talairach.xfm

Hi I got a Talairach Failure Detection Error and therefore did manual registration using tkregister2 following the advice at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview Again following the advice on the site, I re-ran recon-all just to run into the identical error.

Re: [Freesurfer] Mean diffusivity on cortex?

Hello Dr Greve, I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision? Thank you. On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve wrote: You

Re: [Freesurfer] mri_glmfit long_stats_slopes with group

Dear FreeSurfer I have read through a similar question/answer (again): http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53238.html However, i still done seem to understand how to exactly pass the output of long_stats_slopes into the following command with a C and fsgd file??