Re: [Freesurfer] visualizing paths stats by voxel

rerun "trac-all -path" only > for the subjects that have 1 time point. Then rerun "trac-all -stat" with all > subjects together. And then tell us what other problem you find :) > > Best, > a.y > > On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote: > >> Hey An

[Freesurfer] Fwd: visualizing paths stats by voxel

> Begin forwarded message: > > From: Janosch Linkersdörfer <linkersdoer...@gmail.com> > Subject: Re: visualizing paths stats by voxel > Date: 3 Nov 2015 09:37:48 CET > To: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > Cc: freesurfer@nmr.mgh.harva

Re: [Freesurfer] visualizing paths stats by voxel

to be the first, eh? :) Thank you very much, Janosch More soon, a.y On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: Hey Anastasia, thanks for looking into this. Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Looking at the stats files

Re: [Freesurfer] visualizing paths stats by voxel

with a single time point through the longitudinal stream as well? Yes, I ran the longitudinal stream for all subjects, also for the ones with only one time point. Thanks, Janosch Best, a.y On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia, yes, I am. But it looks similar

Re: [Freesurfer] visualizing paths stats by voxel

Hi Anastasia, yes, I am. But it looks similar in the distributed version :( Thanks, Janosch Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Are you by any chance using the dev version of freeview? a.y On Fri, 7 Aug 2015, Janosch

[Freesurfer] Cluster correction in restricted space -- clusters outside of boundaries

Hi all, I have a question/problem related to restricting monte carlo cluster correction to a reduced search space. I have: 1) created a label including the labels of regions I am interested in 2) used mri_mcsim with the --label flag and the label created in 1) to create cached monte carlo

[Freesurfer] use of info from cortical parcellation in TRACULA

Hi Anastasia and others, I am sorry if I just did a bad job, but I could not find information on how information from the cortical parcellation is used in the path tracking done by TRACULA, especially, which cortical labels are used as determinants (seed, waypoint) for which tracts. It would

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Am 03.03.2015 um 14:42 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: Some of this Martin will have to comment on, but my comments below On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote: Hey Doug, thanks again! That means, I would do something like: 1.) construct

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

of the multi-time point subjects before the 1st stage of analysis. doug On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote: Hi Doug, thank you very much for your answer! Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: You would do the long analysis using

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

. Can I still use this method (which would only consider the 3/4 of the subjects) to correct clusters found in the whole group? Or would it only be valid for correcting clusters from an LME model for the reduced group? Thanks, Janosch doug On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote

[Freesurfer] mri_surfcluster questions

Hi all, I experimented with the different flags for mri_surfcluster and have 2 issues that I don't understand, it would be great if somebody could enlighten me: 1) When I set --thmin (or --fdr) with --thsign abs, I get what I would expect, i.e., only clusters with a minimum vertex-wise p-value

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hi Doug and others, I would like apply (Monte Carlo simulation) cluster correction (as opposed to the implemented vertex-wise FDR correction) on the results from a longitudinal study I analyzed using the LME toolbox. The design is unbalanced (different number of time points, from 1 to 4, per

[Freesurfer] use of RFT script for cluster correction of results from lme analysis

Hi Don, Jorge, and list, I would like to do cluster-size based family-wise error correction on the results of a longitudinal analysis done with the lme toolbox. As Jorge told me that if I don't use spatiotemporal models, the use of RFT should be valid, I want to use the script posted on the

[Freesurfer] Rerun Tracula adding CVS registration

Hey Anastasia (and list), I decided to go with affine registration to MNI when I processed my longitudinal dataset with Tracula, because I didn't realize that one has the option to do both MNI and CVS registration in parallel. Is there a way to rerun Tracula with the CVS option without having

Re: [Freesurfer] Rerun Tracula adding CVS registration

registration, so skip those when you run trac-all -prep to save time. Hope this helps, a.y On Mon, 9 Feb 2015, Janosch Linkersdörfer wrote: Hey Anastasia (and list), I decided to go with affine registration to MNI when I processed my longitudinal dataset with Tracula, because I didn't

[Freesurfer] bvallist option in dmrirc file?

Hi, I am trying to process diffusion data with the longitudinal TRACULA stream. I want to specify different bvecs and bvals files per scan in the dmrirc file. For bvecs this is possible using bveclist = ... I tried to use bvallist = ... but apparently this does not seem to work because

Re: [Freesurfer] bvallist option in dmrirc file?

Hi Janosch - Yes, it assumes that all subjects in your study where scanned with the same b-values. What is your situation? a.y On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote: Hi, I am trying to process diffusion data with the longitudinal TRACULA stream. I want to specify

Re: [Freesurfer] bvallist option in dmrirc file?

for statistics along the trajectory of a tract? Thanks a lot, Janosch On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote: Hi Anastasia, I am already preparing separate dmrirc files for different subjects (but including all time points for a specific subject) because that way I can run them

[Freesurfer] Restrict lme analysis results/FDR correction to ROIs from atlas labels

Hi Freesurfers, after running through the longitudinal stream and modeling with linear mixed effect models, I would like to restrict the analysis to only specific ROIs and run FDR correction for vertices included in them. - I think I can do this with mri_surfclusters with the --mask option,

[Freesurfer] Digest mode for mailing list and responding to mails

Hi list, I recently switched to the digest mode for the mailing list. Since then, I don't receive answers to my mails as mails anymore, making it harder to respond to them (or any other mail on the list). Does anybody experience the same issues? How did you solve them? Thanks, Janosch

[Freesurfer] Download of latest Tracula version not possible

Hi all, I am trying to download the latest version of Tracula from this site http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. This seems not to be possible at the moment. Are there server problems? Thanks, Janosch ___ Freesurfer mailing list

[Freesurfer] Tracula mri_convert error

Hi experts, I wanted to play with Tracula. Strangely, already the first preprocessing step, i.e., conversion to .nii.gz, fails. Apparently, mri_convert (falsely) recognizes my dicom files as MGH dicoms (This looks like an MGH DTI volume). Could this be the reason why it fails? Thanks,

Re: [Freesurfer] Changing subject names after processing

Hi Martin and Doug, thanks for your answers! theoretically it would be sufficient to rename the longitudinal directories accordingly as the base should not change at all, only some of the filenames -- not tested! Did I understand it correctly that if one has gone through the whole

Re: [Freesurfer] Changing subject names after processing

and in the long directory names and long/mri/transform files. I think these are all the places where subject names are stored, but no guarantee. Best Martin Sent via my smartphone, please excuse brevity. Original message From: Janosch Linkersdörfer Date:10/26/2014 6:05

[Freesurfer] Changing subject names after processing

Hi all, I wonder whether I can rename subjects after processing has been done and do further processing or stats on them without running in any problems. From reading http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg26244.html, it seems as if the name of the subject folder

[Freesurfer] watershed error again

Hi all, I posted this problem earlier, but did not get an answer, so I am posting it again, sorry! --- recon-all runs smoothly for all my subjects but one. It throws the error mri_watershed Error: indices out of bounds and finishes (see

[Freesurfer] Longitudinal troubleshooting

Hi Martin and all, I am about to process a large longitudinal dataset (normal development, no patients) and wanted to ask about the best (i.e., time efficient) strategy for troubleshooting. If I understand correctly from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits, it might be

[Freesurfer] watershed error

Hi all, recon-all runs smoothly for all my subjects but one. It throws the error mri_watershed Error: indices out of bounds and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log). The image quality does not seem to be different... The error has been discussed on the list

[Freesurfer] Installing only Freeview

Hi all, is there a way, to install only freeview not the whole Freesurfer package (on Mac OS X). Or, alternatively, can somebody please tell me what I can safely remove after installing the whole package to be able to still run Freeview, but save the maximum of hard disk space? I do all

[Freesurfer] Freesurfer version after 5.3.0 from May 2013?

Hi all, I am a little confused about what the latest Freesurfer version is. I thought that v5.3.0 from May 15, 2013 would be the latest, but today I saw in the Tracula update list that there is apparently a version from December 9, 2013. Could you please clear that up for me? Thanks,

Re: [Freesurfer] Freesurfer version after 5.3.0 from May 2013?

Thanks, Anastasia! Am 01.04.2014 um 17:36 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - The December 9th tracula update is just that, an update to the tracula code without any changes to the rest of freesurfer. a.y On Tue, 1 Apr 2014, Janosch Linkersdörfer wrote

Re: [Freesurfer] Troubleshooting - uncertainty about adding control points

modifying the images is a crucial point in the process that influences all further steps, and I just don't yet have a feeling for it... Thanks, Janosch cheers Bruce On Thu, 30 Jan 2014, Janosch Linkersdörfer wrote: Dear Freesurfers, I am just getting started using Freesurfer. I

Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis

Jan 2014, Janosch Linkersdörfer wrote: Hi Bruce, thank you very much for your answer! Am 15.01.2014 um 14:33 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Janosch it will certainly make your life easier if you don't change the names. So the subject names are saved

Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis

the names of the subject folders and/or symlink them to another location (with another name) and continue with further processing. Thanks, Janosch Am 13.01.2014 um 13:34 schrieb Janosch Linkersdörfer notes4ja...@googlemail.com: Hi all, I have 4 years of structural scans from children and 2 from

Re: [Freesurfer] Folder organization cross-sectional/longitudinal analysis

can, e.g., change the names of the subject folders and/or symlink them to another location (with another name) and continue with further processing. Thanks, Janosch Am 13.01.2014 um 13:34 schrieb Janosch Linkersdörfer notes4ja...@googlemail.com: Hi all, I have 4 years

[Freesurfer] Folder organization cross-sectional/longitudinal analysis

Hi all, I have 4 years of structural scans from children and 2 from adults. I would like to analyze the data both cross-sectionally and longitudinally. In the recommendations for the longitudinal analysis, it says one should process all images in one folder with the time point in the

[Freesurfer] mri_convert introduces flip

Hi experts, I´m trying to convert original images in native space from the LPBA40-Atlas (http://www.loni.ucla.edu/Atlases/LPBA40/) from img/hdr to nii/nii.gz. Conversion always results in a left/right flip. Also, mri_convert complains that no .mat file is available but there are no mat files