Re: [Freesurfer] Demeaning variables

Hey Doug, Sorry for keep bothering, today I was trying to do what you told me yesterday, but some doubts arose. I ran QDEC using DODS to see if there were any interactions (significant regions) between age (age variable was not demeaned) and group. I didn’t found anything, no significant

Re: [Freesurfer] Longitudinal TRACULA: mri_convert

Dear Anastasia, I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html). He mentioned that obtaining a new license could solve the issue. It did, so my problem is resolved. Best, Vincent

Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

Hi Antonin, In our experience with FreeSurfer 5.3 we were getting very consistent results. We are going to try some of this locally and work with the FreeSurfer folks to get the T2w stream working robustly in FreeSurfer v6.0+. Thanks for testing this, Matt. From:

Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

Hi Anastasia If I want to use Tracula DTI files instead, which file do I choose: Is it FA_ditifit.nii? Best Knut Jørgen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

Dear experts, given sub-optimal results of my surfaces I referred to in my previous post, I have tested several different settings and input data preparation to obtain optimal pial surfaces in my modified HCP pipeline. I tested all variants in 5 representative subjects. My modified HCP

Re: [Freesurfer] TR : recon-all exited with ERRORS in Talairach

Hello Jean-Simon, If indeed you are running the same subject on the same machine, then the reason its failing has to be because of an update to perl. It's possible your Linux update also updated the version of perl, even if only a minor verion update, and this is what created the issue. You

Re: [Freesurfer] Longitudinal TRACULA: mri_convert

Dear Anastasia, I have checked the image and it looks good. I don't think the image is the problem, especially considering that my issue is also popping up with standard data. See for example the following code: $ echo $FREESURFER_HOME /home/mriuser/privatemodules/freesurfer $ cksum $(which

Re: [Freesurfer] Longitudinal TRACULA: mri_convert

Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA but probably something about the format of your input nifti volume. How did you create that volume? Can you open it in freeview and view it normally? a.y From:

[Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts, I am trying to run longitudinal TRACULA but I am getting an error early on in the process that seems to originate from mri_convert: #- /home/mriuser/privatemodules/freesurfer/bin/trac-preproc #-

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

Doug, can you do me a favor and check to see if this modified version of recon-all works on your data? https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all On 11/30/2016 11:41 AM, Douglas Merkitch wrote: > Hmmm it is a dicom file. Could it be that the lack of file extension > gives it

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

Actually, it is the lack of a dot (".") in the file name. This is a short-coming of recon-all. I'm really surprised that it took this long to manifest itself. The short-term fix is to convert the files to mgz, then pass the mgz files to recon-all. On 11/30/2016 11:41 AM, Douglas Merkitch

Re: [Freesurfer] DTI Multi band sequence?

That would be yet another way. For those that are curious, the field is “MosaicRefAcqTimes”. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department

Re: [Freesurfer] DTI Multi band sequence?

I can't remember the tag numbers, but I believe the time of slice acquisition is in the dicom. You should be able to just pull that field on one volume and compare the field for all slices and see if any of them have the same time. hth d On Wed, Nov 30, 2016 at 12:10 PM, Martin Juneja

Re: [Freesurfer] DTI Multi band sequence?

Hi Martin, I’ve addressed this in your query to the FSL list. Please see my response there. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of

[Freesurfer] DTI Multi band sequence?

Hi, I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine whether the DTI data (in DICOM format) I have is multi-band sequence? I used dicominfo in MATLAB but couldn't find any information related to multi-band in the dicom header. Any help would be really appreciated.

Re: [Freesurfer] longHippoSubfields

We will get the beta for now then. Thanks Eugenio! regards, Christian From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 30 November 2016 15:46 To:

Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

Hi Knut Jørgen - The aparc+aseg doesn't contain the wm-* labels, only the cortical labels from the aparc (in the 1000's and 2000's) and subcortical labels from the aseg. The wm labels (in the 3000's and 4000's) are in the wmparc only. a.y From:

Re: [Freesurfer] longHippoSubfields

Hi Christian, I believe you were unlucky enough to download the dev version during the days that this module was broken. I would strongly suggest that you either download the beta version of 6.0 or wait until the official release of this version, which should be happening soon. Cheers, /Eugenio

[Freesurfer] longHippoSubfields

Dear Juan and FreeSurfer team, We are trying to test out the longitudinal hippocampus subfield segmentation pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We have done the standard processing in v5.3 and have the following dev version:

[Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

Hi, I would like to to obtain FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a DWI file, either produced by dt_recon (or perhaps better - from Tracula) and an anatomy file in atlas space and then use WMParcStatsLUT.txt or