Re: [Freesurfer] QDEC question

Dear Freesurfer experts, Thanks for your valuable input. Since, comparison with global thickness does not provide any valuable information we have decided to forego the average thickness and lh-thickness comparison and now added eTIV as another covariate with age ​ and ​ lh/rh thickess ( ​please s

[Freesurfer] Running A Single Time Point Through Longitudinal Processing

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 poin

[Freesurfer] Automaticky: Jan Sanda is out of the office (příchod 03.08.2015)

Jsem mimo kancelář do 03.08.2015. Poznámka: Toto je automatická odpověď na vaši zprávu "Re: [Freesurfer] if: Expression Syntax" odeslanou dne 24.7.2015 0:05:01. Toto je jediné oznámení, které obdržíte v době nepřítomnosti této osoby. ___ Freesurf

Re: [Freesurfer] assigning 74 Destrieux parcellations into lobes, networks, sensory-motor modalities

As mentioned by Chris, (2) and (3) are not super clear cut, but you can perhaps use my resting-state networks (available in FreeSurfer; https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) as a basic reference. Roughly speaking, for the 7-network parcellation, the blue cluster co

Re: [Freesurfer] if: Expression Syntax

Yes, but you have a typo -min305 instead of -mni305 On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote: > I sure can. Hopefully. Is the what you need? > > > > >> On Jul 22, 2015, at 5:01 PM, Douglas N Greve >> mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> can you just send the log and not put i

[Freesurfer] [FreeSurfer] add to color lut for aparc+aseg.mgz

Hello FreeSurfer world, We need to subdivide regions of the forebrain that FreeSurfer does not. Is it possible to further subdivide regions of the brain on aparc+aseg.mgz by defining new colors (& numbers) on the color lut that already defines structures in Freeview? Thanks so much Joseph Vel

[Freesurfer] Trac-all -stat

Hi, I'm using tracula with stroke subjects with a mixture which hemisphere is lesioned, so I'd like to compare all contra- or ipsilesional hemis together. trac-all -stat combines pathstats.byvoxel.txt for group analysis. Is there a way to combine some subjects' LH tract and other subjects' RH tr

Re: [Freesurfer] Question about pial surface correction through Freesurfer

Hi Kalyan usually improving the wm surfaces results in improved pial surfaces. If not, it typically means something went wrong. If you upload a subject and email me and Ani the coordinates of a spot (or spots) you are having trouble, we will take a look cheers Bruce On Thu, 23 Jul 2015, Trip

Re: [Freesurfer] if: Expression Syntax

Just following up. Did i send the log in the correct format? Thanks, Keji On Jul 22, 2015, at 5:30 PM, Morenikeji Adebayo wrote: > I sure can. Hopefully. Is the what you need? > > > >> On Jul 22, 2015, at 5:01 PM, Douglas N Greve >> wrote: >> >> can you just send the log and not put it int

[Freesurfer] mri_extract_label output

Hi, I would need to extract multiple labels from the aparc+aseg labelmap. I am using the mri_extract_label command, but by default all the labels of the output file are coded with the same number. Would it be possible to change such behavior, and extract multiple labels while assigning different la

Re: [Freesurfer] Question about pial surface correction through Freesurfer

Hi Ani, Thank you so much for your reply. In response to your questions: - This is an error I have been seeing fairly frequently in a subset of my scans, though it varies in its extent. - It seems to be fairly consistently scattered throughout frontal cortex.  - I made a couple of co

Re: [Freesurfer] assigning 74 Destrieux parcellations into lobes, networks, sensory-motor modalities

I have tools in R that can do #1, and network/graph theory analysis on top of that. I plan to work on things like #2-3 but haven't yet (e.g. there is possibly less consensus if region X is limbic vs. para-limbic, as opposed to temporal vs. parietal). I can send you something in a few days/a week

Re: [Freesurfer] bad registration using mri_vol2vol

Thank you Doug I tried the way you suggested and the registration actually looks worse. I also tried: mri_label2vol --subject fsaverage --label /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage_copy/label/$label.label --o $TARGET_DIR/tracy2_$label.nii.gz --reg $FRE

Re: [Freesurfer] Overlapping of aparc.annot labels

HI Alessia you can turn the aparc file into separate labels using mri_annotation2label, then load different parcels as individual labels cheers Bruce On Thu, 23 Jul 2015, Alessia Sarica wrote: > Dear all, > > this is to know if you can suggest me the right way for visualizing on > FreeSurfer

[Freesurfer] assigning 74 Destrieux parcellations into lobes, networks, sensory-motor modalities

Dear FreeSurfer community, I am a statistician who knows shamefully little about brain anatomy and I am writing with a request. I don’t have easy access to Freesurfer and the original data but have the final text output i.e., the /stats folder, from a large cohort, which including *h.aparc.a20

[Freesurfer] Overlapping of aparc.annot labels

Dear all, this is to know if you can suggest me the right way for visualizing on FreeSurfer 3D template, one single label at once, from apart.annot file. Best regards, Alessia Sarica ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma

[Freesurfer] cluster_wise correction

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 maps are generated in two groups, such as Patient and HC. I do the functional connectivity comparison between the tw

[Freesurfer] Using ROIs in SPM

Hi, I found group differences based on T1 images with 8 channel coil in QDEC and for fMRI in SPM I have used T1 images from 32 channel coil for the same subjects . Now I want to use the regions that I found in QDEC for fMRI analysis . Would you please let me know how can I transfer the labels betwe

Re: [Freesurfer] hello freesurfer developer~

1. No, each subject has a different #. You can map to fsaverage (this is what -qcache does if you specify it for recon-all), then they will have the same #. 2. What result data do you mean? 3. Yes, although I'll leave the details to Doug (since I don't remember how his cluster code works).

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

Hi Martin, Just had a quick follow-up on the conversation from yesterday. I already have long_mris_slopes results from tp2-tp1 and tp3-tp1. Going by your previous email, I am going to do a subtraction using mris_calc to get the difference maps and then do an OSGM on the difference maps. Bu

Re: [Freesurfer] Question about pial surface correction through Freesurfer

Hello Kalyan, A few questions: -Is this an error you see frequently in your scans, or just a one-off type of error? -Is it always in the same places anatomically? -Did you make sure to put the control points in areas that were 100% white matter, and that had intensity values < 110 ? If you

Re: [Freesurfer] About reference to zgees_ and ztrsen_

Hi zk, I also looked into the source code and check under the imports in mymatrix.cpp, which are: #include #include #include "MyMatrix.h"#include "Quaternion.h"#include "utils.h" //nint#include #include #include #include #include #include #include #include #include #include #include #inclu

Re: [Freesurfer] About reference to zgees_ and ztrsen_

Hi zk, I did install these packages from centos 6.6 distros but the problem persist some how, i am not sure what I missed Thanks On Tue, Jul 21, 2015 at 1:55 PM -0700, "Z K" wrote: I was able to get around that issue by installing the following packages: lapack-devel.x86_64 libl

[Freesurfer] Error during longitudinal processing

Dear all, I am facing problems in completing the longitudinal pipeline with recon-all. Here is the detail: FS version (downloaded two weeks ago): freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 The longitudinal pipeline given in recon-all was exactly followed as: 1) cross-sectionally pro

[Freesurfer] Controls points not transferred to [LONG]

Dear FreeSurfer group, In a longitudinal dataset i have left the [CROSS] unedited and only edited the [BASE] (i.e. control points and brainmask edits). The brainmask is transferred to the [LONG] but it seems as the control points has not been transferred from the base. There are no control.dat fil