[Freesurfer] MRI_segstats for adc.nii from dt recon - increasing decimal digits

Hi! I ran mri_segstats as instructed in the wiki to extract ADC values from adc.nii. And as you can see below in my output, I think the decimal digits are truncated and missing the following decimal values. Is there an option or other way to get around this problem and extract ADC values from

Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz

I found out why it didn't work. One of the script that bedpostx_postproc.sh calls is written in python2. I set my default to python3 and therefore caused the error in the last step. After I loaded python2 environment, i got the merged files and finished properly. Thanks for your help as

[Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz

Hi Anastasia, trac-all -prep completed without error. I thought trac-all -bedp starts and ends without any error but trac-all path failed with these messages. Loading BEDPOST parameter samples from */dmri.bedpostX niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz ERROR:

[Freesurfer] Tracula ROI analysis CVS vs MNI reg

Hi Anastasia, Is there a preferable method between CVS vs MNI registration when extracting diffusion mesures from ROIs (white matter, ASEG etc)? Best, Yoon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] TRACULA extracting diffusion measures using ASEG or WM parc

Hi Anastasia, Is it possible to extract diffusion measures FA, ADC etc. within the subcortical (ASEG) or WM parc ROI regions using the Freesurfer tools? If possible, can you show how it can be done? Thank you in advance. Best, Yoon ___ Freesurfer

[Freesurfer] Input for mris_fwhm to generate fwhm.dat file

Dear freesurfer experts, This is a follow up question from a previous post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47480.html I have created a sig.mgh from my own stats code and need to also generate fwhm.dat file to run the monte carlo sim, which is estimated from

Re: [Freesurfer] mri_glmfit-sim using custom stat outputs

residual, you can run mris_fwhm to get the fwhm.dat file, and then just > run mri_glmfit-sim. > doug > On 06/02/2016 02:56 PM, Chung, Yoonho wrote: > > Dear experts, > > > This is a follow-up question from my previous post. > > > http://www.mail-archive.com/free

[Freesurfer] mri_glmfit-sim using custom stat outputs

Dear experts, This is a follow-up question from my previous post. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47287.html If I am running stats with my own stats code to generate p-values and other parameters, what other files do I need to generate in order to run

Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

4/2016 01:55 PM, Chung, Yoonho wrote: > > Hi - If I would like to try to perform mass-univariate statistics at > the vertex level (thickness, area, vol at each vertex) without using > the mri_glmfit, is this order a sound step (in general) for mapping > stats parameter of choice (p-val

Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

Yes - I am interested in applying the monte carlo sim to my own model fit. Doug can you walk me through the steps I need to get this part done? When you say residuals, I am assuming that I need to supply a vector file of residuals after I fit my model to the smoothed data (eg. using

[Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

Hi - If I would like to try to perform mass-univariate statistics at the vertex level (thickness, area, vol at each vertex) without using the mri_glmfit, is this order a sound step (in general) for mapping stats parameter of choice (p-val or t s or weights for example) to the surface? 1. Use

[Freesurfer] tractstats2table for dwi motion

Hi Anastasia, I was wondering if there is a flag in the tractstats2table function that extracts all the variables in the dwi_motion.txt file for all subjects and put them into a single spreadsheet. Thanks! Best, Yoon ___ Freesurfer mailing list

[Freesurfer] Hippocampal Subfields missing nonPartialVolumeStatsRight.txt file

Hi, I am running Hippocampal subfield processing stream and I think I got all the appropriate posterior_*.mgz files I need to get the stats, but I am not seeing nonPartialVolumeStatsRight.txt anywhere as described in the wiki under $subjectsdir. What I am seeing is volumeStats_left.txt and

[Freesurfer] Steps for Longitudinal trac-all

Dear FS experts. I am trying run trac-all - the longitudinal version - on the cluster and not by using the dmrirc file. I am looking at the 'trac-all -help' and also the wiki, but I couldn't find a flag or option where I could specify the use of unbiased-template (e.g. [subjectID-base]) and

[Freesurfer] New longitudinal Tracula version?

Dear Freesurfer Experts We decided to reprocess our T1 and DTI data with the latest stream v.5.3 – we would like to give TRACULA longitudinal stream a try. Before we go ahead and reprocess our recons and DTI data with FS v 5.3 we were wondering if you plan to release a new version of the

[Freesurfer] Update to Tracula longitudinal?

Dear Freesurfer Experts We decided to reprocess our T1 and DTI data with the latest stream v.5.3 – we would like to give TRACULA longitudinal stream a try. Before we go ahead and reprocess our recons and DTI data with FS v 5.3 we were wondering if you plan to release a new version of the TRACULA

[Freesurfer] freesurfer v5.3 TRACULA longitudinnal error

Hi Anastasia I switched from FS v.5.2 to v.5.3 and I am still having this error when running TRACULA longitudinal freesurfer stream despite running with freesurfer v5.3 (both recon-all and trac-all). I am sending along the dmrirc file and the log file. Could you check what may be causing this

Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal

Thanks for the tip. Another question. In the dmrirc file, can we also define multiple bval file? (like how in the example-dmrirc long- you can set multiple bvecs.txt using 'set bveclist'? In the example, option for specifying multiple bval files is not shown. Thank you Yoon On May 22,

[Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal

Hi Anastasia, I have a large set of freesurfer recons (T1) already processed through FS version 5.2 longitudinal stream while ago. However, I see now that there is an advantage of using Tracula 5.3 longitudinal stream for DTI longitudinal analysis. Do you know if I run the DWI data using 5.3

[Freesurfer] aparcstats2table for multiple labels

Dear fs experts, I have created 5 customized labels that I want to extract mean thickness from each subject. Is there a way to generate a text file for all the labels I made? For example, aparcstats2table --parc option only allows to read one label at a time. I am wondering if there is a way

[Freesurfer] Effect size

Hi all, Where can I find the effect size file(.mgh) after running mri_glmfit when doing group analysis (control vs patients adjusting for age and sex)? Somewhere in the wiki said gamma.mgh is the surface overlay for effect size. Is this true? If not, how would I compute one? Yoon

[Freesurfer] t-statistics map using tksurfer

Dear all, Is there a way to visualize vertex wise t-values (t-statistics), instead of p-values, on a vertex map when you are doing group analyses? I successfully generated the p-maps using mri_glfmfit, but I am wondering if vertex-wise maps that represent t-values can be also generated and

[Freesurfer] Average absolute symmetrized percent thickness change

Dear Freesurfers, Is there a way to visualize average absolute symmetrized percent thickness/volume/area change (not significance map) using qdec or tksurfer or other freesurfer tools? I successfully generated correlation significance map using qdec for the longitudinal data we processed, but

Re: [Freesurfer] Average absolute symmetrized percent thickness change

cc'ed Nick who probably knows more). If qdec cannot do it, you can probably find the gamma.mgh file in the glm/constrast subdirectory and then open it with tksurfer. Best, Martin On 08/30/2013 02:16 PM, Chung, Yoonho wrote: Dear Freesurfers, Is there a way to visualize average absolute

[Freesurfer] Longitudinal processing - Surface area

Dear all, I am interested in looking at developmental changes in the brain during adolescence period in normal subjects and also comparing our controls to our clinical patients. Examples in the longitudinal processing stream tutorial have only mentioned volume and thickness, so I was wondering