Re: [Freesurfer] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log

Nick, Thanks for your kind help. I uploaded my orig.mgz i.e. 001.mgz using Martinos center file drop. Thanks Venkat On Mon, Jun 23, 2014 at 11:42 PM, Nick Schmansky, MGH < ni...@nmr.mgh.harvard.edu> wrote: > Venkat, > > Can you send me your orig.mgz so that I can attempt to replicate? > > Nick

[Freesurfer] problem with qdec stats tables

Dear mailing-list, I’ve got a question concerning the file types of stats tables in qdec. After generating the stats tables there are two files e.g. lh.aparc.a2005s.area.stats and lh.aparc.area.stats. Which one is the right one to work with ( statistical analysis)? How do they differ in character

[Freesurfer] fMRI Image Acquisition and Analyses Course : October 16-18, 2014 (fwd)

FYI -- The Mind Research Network (MIND) is pleased to invite you ​​to the fMRI Image Acquisition and Analyses Course held on October 16-18, 2014 on the campus of the University of New Mexico in Albuquerque, New Mexico. For more information and registration, see http://www.mrn.org/education-outr

Re: [Freesurfer] recon-all ERROR, no idea why

Thanks Douglas, I definitely appreciate your help. Here is what it Spit out, *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University *www.NeuralControl.net *

Re: [Freesurfer] hippocampal subfields in young subjects

Dear Koen and Freesurfers, I haven't receive any further replies regarding the black lines surrounding the subfields I found in the sample of subjects I am analyzing. As I said the subjects are quite young (9-14 years of age) and I visualized the subfields with Freeview. Do you have any idea why

Re: [Freesurfer] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log

Venkat, Can you send me your orig.mgz so that I can attempt to replicate? Nick On Mon, 2014-06-23 at 08:46 +0530, Venkateswaran Rajagopalan wrote: > Hi Bruce, > > > Thanks very much. I will wait for Avi Synder's response. > > > Thanks a lot > Venkat > > > On Sat, Jun 21, 2014 at 8:23 PM

Re: [Freesurfer] RAS to voxel transform

Your interpretation is not correct. RAS always means that R is pos x, A is pos y, and S is pos z. That is the voxel-to-RAS transform. Here voxel means column-row-slice. So this matrix takes a col, row, slice and converts it into a RAS. So that first negative 1 means that as the column number i

Re: [Freesurfer] QDEC Error loading the data table

Hi Doug, I did create them in windows. I will recreate them on the linux machine and carry out the processing. Thanks for the help. Mohammed On Mon, Jun 23, 2014 at 1:38 PM, Douglas N Greve wrote: > > That does look pretty silly. How did you create your qdec.table.dat and > level files? If yo

[Freesurfer] RAS to voxel transform

Hi, I'm trying to understand the conversion from RAS (freesurfer surface coordinate) to volume space (x, y, and z.. According to Graham Wideman documentation here http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm (if it is not outdated), Right is negative x, *Anterior is positive z*, an

Re: [Freesurfer] A comparison between atlases

On 06/23/2014 01:35 PM, Dorian P. wrote: > Thank you Bruce and Douglas, > > I meant to combine them because I did not want overlaps. I don't think we have any tools to mix and match them. > > Can I advance one more question as we are here. How can I get an > average thickness of the entire latera

Re: [Freesurfer] QDEC Error loading the data table

That does look pretty silly. How did you create your qdec.table.dat and level files? If you created them under windows, then that could be the problem. If not, post your qdec.table.dat file and the gender.level file and I'll take a look On 06/23/2014 01:33 PM, Mohammed Goryawala wrote: > Hello

Re: [Freesurfer] A comparison between atlases

Thank you Bruce and Douglas, I meant to combine them because I did not want overlaps. Can I advance one more question as we are here. How can I get an average thickness of the entire lateral temporal lobe (inferior, medial, temporal gyri)? The average of the three gyri may not be useful as one gy

[Freesurfer] QDEC Error loading the data table

Hello FreeSurfer Experts, I am trying to run QDEC for a group comparison study. I am following the tutorial found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview However, when I try to load my data table it returns the error.

Re: [Freesurfer] Why the result was not same for the same subject

yes, that was our goal some time ago and we thought we had succeeded in tracking down and fixing any randomness if the same seed is specified Bruce On Mon, 23 Jun 2014, Harms, Michael wrote: > > Actually, if you run 'recon-all' a second time (from scratch) on the same > subject, on the same pl

Re: [Freesurfer] A comparison between atlases

>>For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation? Not by default, bu you can create one easily enough with cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009

Re: [Freesurfer] Why the result was not same for the same subject

Actually, if you run 'recon-all' a second time (from scratch) on the same subject, on the same platform/architecture, and you use the default recon-all settings (i.e., don't use the -randomness flag, or specify your random seed via the -rng-seed flag), then you should get identical results, becaus

Re: [Freesurfer] Fwd: surface to volume visualization

Hi James Ruopeng is traveling and may not answer quickly, although Louis might be able to help Bruce On Mon, 23 Jun 2014, james pardon wrote: Sorry if you are receiving this for the second time , not really sure if this went through the first time I sent the email: Dear all,  I'm looking fo

Re: [Freesurfer] A comparison between atlases

Hi Dorian you don't need to combine them in any specific way if all you want is to look at ROI-based stats. Just take the ones from each atlas that you like. cheers Bruce On Mon, 23 Jun 2014, Dorian P. wrote: Dear Freesurfer followers/developers, I am doing a study involving temporal lobes

Re: [Freesurfer] Extracting mean diffusivity values from diffusion data in freesurfer 5.3

Was this ever answered? 1. Units - Not sure what the units of MD are. It might depend on your b-value 2. MD is not constrained to be between 0 and 1. Where are you getting that? 3. I don't know about the CC values. The CC ROIs are pretty small, and you might be getting significant partial volum

Re: [Freesurfer] Why the result was not same for the same subject

There of course is some variability in the analysis due to the way the segmentation happens. Your results are certainly not out of the ordinary for the volume you are viewing. On average you can expect a ~1% variance between several scans of the same subject. If you want to know more I certainl

[Freesurfer] Fwd: surface to volume visualization

Sorry if you are receiving this for the second time , not really sure if this went through the first time I sent the email: Dear all, I'm looking for a way to automate surface on volume visualization, to check if the surface reconstruction have been successful on a very large number of subjects.

[Freesurfer] A comparison between atlases

Dear Freesurfer followers/developers, I am doing a study involving temporal lobes and the parcellations from Desikan and Destrieux atlases have very different results. I like the full gyrus parcellation of Desikan but the temporal pole is very small and limited, while in Destriux the temporal pole

Re: [Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint

How did you convert to mgz? Did you start with dicoms and use mri_convert? How do you know they are flipped? On 06/23/2014 12:56 PM, Chiu, Bryan (PHTH) wrote: > Hi, > > I'm attempting to do some longitudinal processing on a set of data > with subjects with up to 4 timepoint scans: Baseline, M

[Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint

Hi, I'm attempting to do some longitudinal processing on a set of data with subjects with up to 4 timepoint scans: Baseline, Midpoint, Final, 12 months after Final. When visually checking over a subject in Freeview, I notice that all of my Midpoint runs are left-right flipped, where the other

Re: [Freesurfer] Retinotopic mapping using selxavg3-sess

Yes. I'm surprised that FSL would run at all without that defined. doug On 06/23/2014 12:44 PM, Alan Lee wrote: > Yes, I've installed FSL already. I can launch FSL by typing "fslview" > in the command window. > > However, it seems that the $FSLDIR is not defined. Should I define it > manually u

Re: [Freesurfer] Retinotopic mapping using selxavg3-sess

Yes, I've installed FSL already. I can launch FSL by typing "fslview" in the command window. However, it seems that the $FSLDIR is not defined. Should I define it manually using setenv before running selxavg3-sess? -- Alan Lee sites.google.com/site/alanlflee/ On Mon, Jun 23, 2014 at 4:03 PM

Re: [Freesurfer] recon-all ERROR, no idea why

can you run the command below and send nu.log? cd /media/sf_Imagery/FreeSurfer/xx/mri mri_nu_correct.mni --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz |& tee nu.log On 06/23/2014 11:49 AM, Remy Wahnoun wrote: > hello, freesurfers, > Im having troub

Re: [Freesurfer] Why the result was not same for the same subject

Wang, what command-line flags were included? can you send me the recon-all.log file for these runs? The results should be the same with repeated runs if the default flags were used. Nick On Jun 21, 2014, at 10:20 PM, wangkangcheng_gmail wrote: > Dear Bruce > > Yes. The following is an

[Freesurfer] recon-all ERROR, no idea why

hello, freesurfers, Im having trouble using recon-all, I tried the prebuilt virtual machine and a fresh unbuntu install without luck. Would anyone have a look at my recon-all.log? I cant spot any error. *Thanks * *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute a

[Freesurfer] Edits, where art thou?

Hi! When I edit my data, for instance wm editing, I do not see the changes applied to the original image. To make you understand what I do: Open up freeview, load the image, Wm and brainmask, with wm at the top. Then I go into voxel edit, press recon edit, and start filling in topographical defect

Re: [Freesurfer] Basename error

Hi Doug, Thanks very much for the information. I will try it. XIaomin > Date: Mon, 23 Jun 2014 09:19:20 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Basename error > > If it is not using the basename.m in freesurfer it may fail. Try put

Re: [Freesurfer] Vertex analysis cluster values

Hi Rachel, are you saying that there does not seem to be an effect in the mean using the same contrast that was used to compute the clusters? How are you doing the test in the mean? Are you sure you have the same design and contrast matrices? doug On 06/06/2014 02:38 PM, Rachel Jonas wrote:

[Freesurfer] surface to volume visualization

Dear all, I'm looking for a way to automate surface on volume visualization, to check if the surface reconstruction have been successful on a very large number of subjects. Normally, I would use freeview with -f and -v flags to check and see if it is necessary to edit controls points, etc. As an

Re: [Freesurfer] How to extract significant result for each subject

If you run mri_glmfit-sim, it will extract this for you. Run it with --help to get more information doug On 06/12/2014 10:53 PM, kangchengwang0...@gmail.com wrote: > Dear freesurfers, >I contrast depression and control and find that patients have a > lower thickness in region of inferior fr

Re: [Freesurfer] Labels to annotation

Don't use FreeSurferColorLUT.txt, you need to create your own color table whose format is like FreeSurferColorLUT.txt doug On 06/20/2014 03:49 AM, Karen Marie Sandø Ambrosen wrote: > Hi Bruce, > > When I input all the labels in the mris_label2annot command I get the > result shown in: H09_copy_

Re: [Freesurfer] Project probabilistic connectivity maps to pial and calculate mass center

I'm not sure all that you are trying to do, but if you have a registration that maps to the orig.mgz, then you can use mri_vol2surf to map to the pial surface. Run it with --help to get more info doug On 06/20/2014 12:26 AM, gong jinnan wrote: > Dear all, > I have used probabilistic tractograp

Re: [Freesurfer] Group analysis over different studies?

Sorry, yes, I meant ces instead of gamma. It is not set up to use CVS. On my todo list... On 06/17/2014 03:13 PM, Terri Scott wrote: > Hi Doug, > > Is gamma.mgh the same as ces.nii.gz? I'm working with data processed > with an older version of Freesurfer, not exactly sure which. I have a > rel

Re: [Freesurfer] Retinotopic mapping using selxavg3-sess

Do you have FSL installed? If so, what is your $FSLDIR? On 06/19/2014 03:03 PM, Alan Lee wrote: > > Thanks, Doug. I think I've kind of sorted that one out by creating a > folder called "Retinotopy" under > freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... > 004/ folders cont

Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points

This is a bug in QDEC. I'm surprised it has not surfaced before. It is supposed to be looking in "fwhm09" not "fwhm9". One work-around is to create a symlink, ie, cd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/ ln -s fwhm09 fwhm9 otherwise, you will have to run mri_glmfit-s

Re: [Freesurfer] some questions about optseq

I think this is an error I fixed a few months ago. Try this version (for linux) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2 On 06/20/2014 09:05 PM, charujing123 wrote: > Hi doug, sorry for not enough information sending to you. > optseq2 --ntp 223 --tr 2 --psdwin 0 20

Re: [Freesurfer] low polygon count like fsaverage3

Hi Kai you mean you want to decimate the surface? You can use mris_make_face_parcellation to map something like fsaverage3 to your subject. cheers Bruce On Mon, 23 Jun 2014, Kai Schlamp wrote: > Hello again, > I am still looking for a way to create a low polygon surface during > recon-all (w

Re: [Freesurfer] Basename error

If it is not using the basename.m in freesurfer it may fail. Try putting $FREESURFER_HOME/fsfast/toolbox first in your matlab path On 06/22/2014 02:52 PM, Xiaomin Yue wrote: > Hi Doug > > Thanks for you response. The command line is: selxavg3-sess -s > subject_0101 -d . -analysis DoD_looming_l