[Freesurfer] Citing bbregister in articles

Hi, Just a quick question to the Freesurfer creators : how could I cite the bbregister command line in an article ? I didn't find the correct article in the Freesurfer Wiki. Thanks, -- Christopher Coello, Ph.D. Preclinical PET/CT unit Institute of Basic Medical Sciences Faculty of Med

[Freesurfer] Binary volume to surface _ mri_vol2surf

, it returns an error message : freeview -f lesionMask_surf.mgh ERROR: MRISread: cannot read surface data from file /home/epilepsy/sorted/P061/preMR/lesionMask_surf.mgh! Segmentation fault What did I miss ? Thanks for your help, -- Christopher Coello, Ph.D. Preclinical PET/CT unit Institute of

Re: [Freesurfer] Binary volume to surface _ mri_vol2surf

be able to do simple measurments on these mri_vol2surf outputs ? Transform to surface, but how ? Thanks in advance, Christopher > The output of mri_vol2surf is not a surface but an overlay on a surface. > You will need to run something like: > > freeview -f > $SUBJECTS_DI

Re: [Freesurfer] Binary volume to surface _ mri_vol2surf

obtain M1_surf and M2_surf. I would like to measure the area common to M1_surf and M2_surf. Best, Christopher On 11.03.2013 18:12, Douglas Greve wrote: > Hi Christopher, I'm not sure I understand your question. What do you > mean by "simple measurements"? > doug &

[Freesurfer] Cognitive neuroscientist wanted for open position in drug discovery (Cambridge, MA)

Dear Freesurfers, We are looking for a cognitive neuroscientist to join our growing team in the Neurocognition and Functional Imaging group at Pfizer (Cambridge, MA). Please feel free to forward this listing to interested parties or other lists. See the full job posting or apply via https://www.l

Re: [Freesurfer] Tracula: missing or incomplete tracts

What about: freeview -v FA.nii.gz -v V1.nii.gz:vector=yes From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, March 17, 2015 11:57 AM To: Freesu

[Freesurfer] missing files in fsaverage folder

Dear Freesurfer Experts, is there an easy way to update only folders within the Freesurfer folder? Accidentally, I deleted the fsaverage folder from the Freesurfer version. I copied the fsaverage folder from another Freesurfer installation. But seemingly some essential files (e.g. perirhinal la

Re: [Freesurfer] Freesurfer and Tracula installation.

Have you tried these steps: http://wiki.centos.org/TipsAndTricks/NTFS From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fatma Zribi [zribi.fa...@gmail.com] Sent: Thursday, April 23, 2015 9:14 AM To: freesurf

[Freesurfer] computing cluster overlap

tions, but maybe there are much better ways? I'm thankful for any advice, Best wishes, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] Vertex Index to Vertex RAS withouth using surface visualizer (tksurfer or tkmedit)

script the translation from Vertex Index to Vertex RAS Best wishes, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the

[Freesurfer] mri_vol2surf nii.gz to .mgh conversion

WARNING: the voxel resolution in the source volume (1,1,1) differs from that listed in the registration file (2.29167,2.29167,2.99) Reading surface /home/christopher/subjects/PM_04001/surf/lh.white Done reading source surface Reading thickness /home/christopher/subjects/PM_04001/surf/lh.t

Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

to transfer the surface nii.gz files into .mgh files used in volume space? Thanks, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Donnerstag, 2. Juli 2015 14:49

Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

$FREESURFER_HOME/FreeSurferColorLUT.txt --id 410 -id 407 --i $sub/bold/EX.sm5.lh/EX/ces.lh.mgh --maskthresh 2 --masksign abs The ROI analysis always ends up with zero hrf-amplitudes. I appreciate your support, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun

[Freesurfer] Supratentorial Volume Versus Sum of Parts

7;t specific regions we're interested in, they still all look low. How can we explain or understand these situations? It seems like the parts should be close to or equivalent with the whole. Thanks, Washington University in Saint Louis Medical School

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] Supratentorial Volume Versus Sum of Parts

about half of the supratentorianotvent reported by FS, and with ventricles the ratio gets closer to 0.6 rather than half. Thanks, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] Huge difference ini area for the same subject {Disarmed}

Doesn't that just mean your colleagues are editing the brains differently? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of amirhossein manzouri [a.h.manzo...@gmail.com] Sent: Tuesday, July 28, 2015 7:33 AM To: Do

Re: [Freesurfer] Using FSL commands through Matlab (Linux)

Just use either "system" or the exclamation mark and type the FSL commands From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Albrecht, Daniel S. [dsalbre...@mgh.harvard.edu] Sent: Tuesday, August 04, 2015 4:36 PM T

Re: [Freesurfer] Using FSL commands through Matlab (Linux)

Ah, that's probably correct. I think it worked on my system because I source the FSL conf file in my .bashrc From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sen

Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

Andre, I haven't done any statistical comparison, but for my data (pediatric) I found the DKT labels to be somewhat more accurate. The biggest differences were in superior frontal and rostral middle frontal. Other differences I've seen are anterior cingulate, cuneus, and fusiform. See Figure 4 i

Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory

I think it's a bit unclear what you're asking for. Have you followed the tutorials on the wiki? Can you post your directory structure? What I do on my system is keep studies separate from one another. Each study directory has its own FS directory, and I keep the raw images separate. So somethin

Re: [Freesurfer] Computing SA from an older FS version

1. Yes, I would expect that 2. Because the pial surface is bigger. (Unless I'm misunderstanding the question?) From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gerrits, Niels Sent: Thursday, August 27, 2015 10:36 AM To: Freesurfer support list Subje

Re: [Freesurfer] Comparing lists of activated regions between task>ctrl contrasts

>From your original mail: I agree with Dr. Kanwisher. When you ask if it is >appropriate to "(visually) compare" list of regions, I would answer that it is >absolutely not. A direct comparison is necessary. See e.g. Nieuwenhuis et al., >2011, Nature Neuroscience. For your second, I would say t

Re: [Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

Yes, they are 2 separate atlases. The references are on the FS wiki. The "ctab" files are colortable files, so I believe the "25 100 40 0" are the RGB + transparency/opacity From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard

[Freesurfer] epidewarp.fsl radian phase range error

problem. Can I rescale the phase images? I appreciated any support. Best, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for

[Freesurfer] Segmentation Fault with mri_convert

I'm trying to convert the dicom to the original 001.mgz file using the following command on a Mac OSX Yosemite version 10.10.5. My SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/ . My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/ . The following i

[Freesurfer] Segmentation fault in mri_convert

I'm trying to convert the dicom to the original 001.mgz file using the following command on a Mac OSX Yosemite version 10.10.5. My SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/ . My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/ . The following i

[Freesurfer] Research Position

Hi Freesurfers, I wanted to bring to the attention of recent graduates a research assistant position in my lab. Briefly, the position entails the application and transfer of your proficiency with FreeSurfer in the acquisition and analysis of fMRI data collected from healthy adults. More detail

[Freesurfer] bbregister surfaces

Hi all, According to https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html, bbregister uses the white matter surface and cortical thickness measures to perform its registrations, though there was some possibility of using the pial surface in further releases. I just want to ver

Re: [Freesurfer] aparc.DKTatlas40

You can read about it here: http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2012.00171/abstract From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of krista kelly [krista.kell...@gmail.com] Sent:

Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho

I only have anecdotal evidence based on 4 subjects, but I found that using the FLAIR results in much better surface reconstruction than the multiecho. In my experience (with kids age 12-16), the pial surface was underestimated when I used the multiecho.

[Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

distances? *https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017866.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-April/017866.html> I'm a quite Surfer-newby. So sorry for that maybe stupid question... Thank you in advance, Christopher Christop

Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

ple in the middle of the cortical ribbon (to account for drain vessel effects). According to the intended distance measures, relative measures between peak voxels are also fine. So, maybe mris_pmake is still a good option... Greets, Chris Christopher Milde, M.Sc. Biol. Institute for Cognitive an

Re: [Freesurfer] glmfit with correlated covariates

I don't want to speak for the Freesurfer team, but I am 99% certain that it is Direct/Standard as you list them. There isn't any stepwise variable selection going on. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] o

[Freesurfer] native or fsaverage spherical space for distance measures?

rganization) - Do you have any suggestions which procedure is preferable?? - *Am I right about the comparability of distance measurements between subjects, when using mris_pmake within a common spherical coordinate space?? I appreciate any helpful comment Sincerely yours, Christophe

[Freesurfer] interhemispheric registration in native space

, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent

[Freesurfer] Graph theory analysis in R

Dear Freesurfer users, (apologies for cross-post) I am pleased to announce the release of an R package I created, called "brainGraph", for performing graph theory analyses of brain MRI data. You can use it for cortical thickness, volume, surface area, or LGI. It can also be used for tractograph

[Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

Hi, I'm attempting an inaugural run through the FS pipeline on some event-related data collected over 6 runs. I'm not sure if this makes any difference, but the experiment is self-paced, and the events are of varying duration (it's a lexical decision task, and participants can take up to 4 secon

Re: [Freesurfer] Unknown option DKTatlas40

The option should be: --annot aparc.DKTatlas40 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman [marmaduke.wood...@univ-amu.fr] Sent: Wednesday, March 2, 2016 08:27 To: freesurfer@nmr.mgh.

[Freesurfer] preproc-sess error opening tmp brain_mask

I was hoping the developers might be able to help with a problem I'm having with a sub-step of preproc-sess. I executed the following: preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold In the relevant output, I see mktemplate-sess completed, followed by a call to mkbra

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

on another dataset (but on another workstation, but neither were those two binaries to be found on that workstation). Is your /tmp space full? On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote: > > I was hoping the developers might be able to help with a problem I'm > having with

[Freesurfer] ERROR: DOF=0 in call to mri_glmfit by preproc-sess

Hi, First, thanks to Doug Greve for helping me isolate my previous problem, which turns out to have resulted from a conflicting fsl installation. Now that that's resolved, I'm having a problem on a first-level analysis. In preparation for calling selxavg3-sess, I am running preproc-sess on an

Re: [Freesurfer] ERROR: DOF=0 in call to mri_glmfit by preproc-sess

?That seems to have been the problem: Running the data through Slicer as suggested elsewhere fixed the slice time code, but then saved only a single frame of the 4D data. I had been poking around the file header looking for a corresponding field, not suspecting that it was a calculated value and

[Freesurfer] External Regressor of Interest in FS-FAST

The references to external regressors in mkanalysis-sess are a little sparse on how I would go about analyzing a continuous regressor: I have a mixed design experiment: TaskBlock1 Rest TaskBlock2 Rest … TaskBlockN Rest x6 Runs Within each block are jittered events (5 of condition A, 5 of conditi

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Looking at the image posted previously. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn I think it is pretty clear the 5.1 picture has better gray/white contrast. It is a very subtle difference, but you can see it if you look at some pieces of wm that were "missed" by 5.2 in this

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

The 5.2 image has been smoothed, by a small degree, relative to 5.1. Either prior to FS processing or by FS, it would seem. On Mon, Apr 15, 2013 at 3:29 AM, Christopher Bell < christopherbell2...@gmail.com> wrote: > Looking at the image posted previously.

Re: [Freesurfer] pial surface with FLAIR

Hi Veronica, Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"? And then, when you do the remaining recon-all steps: recon-all -autorecon3 -s $SUBJECT -FLAIRpial It has worked for me. (And worked very well! No edits necessary for the pial surface!) ___

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

: Saturday, June 01, 2013 4:21 PM To: Watson, Christopher Cc: Freesurfer Subject: Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2 Hello list, we found the problem, symbolic links: /home/glerma/ is the home of the app server where fs is installed. /home/glerma/glerma/freesurfer/subjec

Re: [Freesurfer] mris_preproc --qdec-long problem

ing on all OS), > let me know. This is the command I use: > > cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") > printf("%s.long.%s\n", $1, $2)}' > > to generate the subjects id's from the table's first two colum

[Freesurfer] freesurfer registration

Hi, I understand that the recon-all script registers and then averages two anatomical images (after bias field correction) if two are provided in the "orig" folder, before performing the other parcellation stages. I am writing a report and it might be good to mentioned what registration is used

Re: [Freesurfer] Painting voxels vs. adding control points

1) The right panel shows the aseg voxels. The surfaces are the same in L and R panels. 2) What do the surrounding slices look like? It may be that the WM surface "fills in" more as you go along. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-bo

Re: [Freesurfer] different results between 5.1.0 and 5.2.0

I don't know, but I'm pretty sure the Freesurfer team will recommend you use v5.3.0. There are emails saying as much. Chris From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of clarissa yasuda [clayas...@gmail

Re: [Freesurfer] trac-all inquiry

I've found that when using the Bash shell, putting multiple subjects in the config file doesn't work. Maybe that's the issue here? Although, I simply never bothered to look into it any more. Chris From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer

Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu

Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Indeed. It's actually really easy to set up, too. From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Frees

Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

yours look particularly good). Is this a noisy dataset or something? From: Joana Braga Pereira [jbragapere...@gmail.com] Sent: Thursday, September 05, 2013 9:32 AM To: Watson, Christopher Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfe

Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Try this: http://www.mail-archive.com/search?q=reinit&l=freesurfer%40nmr.mgh.harvard.edu From: Joana Braga Pereira [jbragapere...@gmail.com] Sent: Thursday, September 05, 2013 9:51 AM To: Watson, Christopher Cc: Anastasia Yendiki; freesu

Re: [Freesurfer] tool to compare surface files (along the lines of diff)?

You could probably load them in matlab and compare there. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Romano [drom...@stanford.edu] Sent: Thursday, September 05, 2013 8:01 PM To: freesurfer@nmr.m

Re: [Freesurfer] recon-all for multiple subjects

The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to. ___

[Freesurfer] parcellations to fmri space

Hello Freesurfers, I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large v

Re: [Freesurfer] nu_correct problem

I believe this post slipped through the cracks. Anyone have any thoughts on this nu_correct error. Some subjects ran fine, so it seems to be an intermittent problem and not an installation problem. Also, is this possibly related to the avi_talairach/intensity normalization issues being discussed i

Re: [Freesurfer] MPRAGE intensity variations

Thanks, Chris From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Saturday, July 14, 2012 5:29 PM To: Watson, Christopher Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MPRAGE intensity variations Hi Chris Are you using prescan normalize? It helps a lot Che

Re: [Freesurfer] parcellations to fmri space

2012 at 9:03 AM, Douglas N Greve wrote: > > Hi Chris, I don't think there is such a tool. One thing you can do is to > use the aparc+aseg.mgz as the source instead of the lh and rh surfaces > separately. This might solve all of your problems. > doug > > > On 07/0

Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

Hi Doug et al, The 2nd question is something I've wondered about. Doesn't a Bonferroni correction assume that the measures are independent? If so, I think in the case of subcortical structures, it is incorrect to use this method, as e.g. the putamen and pallidal volumes are not independent of

Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

ed? Thanks, Chris From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Saturday, July 21, 2012 12:01 PM To: Watson, Christopher Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC Hi Chris, bonferroni will be o

[Freesurfer] CSF segmentation and cortical ribbon

question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ? Thanks a lot in advance, Best, -- Christopher Coello, Ph.D. Preclinical PET/CT unit http

Re: [Freesurfer] CSF segmentation and cortical ribbon

g what you want, but you > could probably get close with some rules. Sounds like the voxels you are > referring to are CSF or dura given their proximity to brain > cheers > Bruce > > > On Wed, 25 Jul 2012, Christopher Coello wrote: > >> Dear Freesurfer users, >> &g

Re: [Freesurfer] CSF segmentation and cortical ribbon

Hi Bruce, Thanks for the reply. I'm not really familiar with compiling C functions, I have been working all the time with Matlab. Always worth to ask : do you have such set of C functions in Matlab also ? Christopher On 25.07.2012 16:10, Bruce Fischl wrote: > Hi Chris, > >

Re: [Freesurfer] TRACULA -prep error

I've just taken to making the sym links myself after running trac-prep and before running bedpostx. Then everything should run normally. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [

[Freesurfer] Whole Brain Volume

Hello All, We are looking into alternative measures for whole brain volume to use for covarying, and the previous topic mentioned mris_volume as a possibility but it isn't located on the top of the aseg file. Has it been moved? Chris McCarthy ___ Frees

[Freesurfer] Dynamic PET _ Time frame averaging

don't see any option for averaging. Thanks for your help, Best, -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +47451

Re: [Freesurfer] Dynamic PET _ Time frame averaging

Works fine. Thanks Doug. On 05.10.2012 18:37, Douglas N Greve wrote: > Hi Christopher, > try mri_concat 4dvolume.nii --mean --o 3dvolume.nii > doug > > On 10/05/2012 03:05 AM, Christopher Coello wrote: >> Dear Freesurfer community, >> >> Just a simple questi

[Freesurfer] Error with mris_calc

.1.37.2.4 2011/04/04 freeview : v1.0 2011/05/22 Best, Christopher -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516

Re: [Freesurfer] Error with mris_calc

binF2 were absolutely not modified, the input volume was "shifted" (see why below) so that the resulting volume was different from what we expected when seeing the overlay in freeview. Best, Christopher On 12.10.2012 16:57, Bruce Fischl wrote: > Hi Christophe > > what does mri

Re: [Freesurfer] TRACULA some fiber volumes being too small

There were recently a few messages on the list regarding this. What you should do is include "set reinit=1" in your config file, and then run trac-all -priors -c $CONFIG trac-all -path -c $CONFIG Make sure you only include the pathway of interest in the config file; otherwise, it will re-run the

Re: [Freesurfer] Red Hat Enterprise Linux 6?

I've had no problems with it. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Brain Apprentice [bapprent...@gmail.com] Sent: Tuesday, November 20, 2012 11:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject:

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

Hi Bruce, So would you recommend acquiring a T2 in addition to an (ME)MPRAGE/SPGR? i.e. is it worth squeezing another acquisition into a protocol? Chris From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bru

Re: [Freesurfer] Cortical thickness analysis on data acquired from multiple sites

Hi Bruce, What if she created an FSGD file, and instead of just having "patients" and "controls", she would have "patients1.5", "patients3", etc.? With over 400 subjects this should be feasible, i.e. the loss of d.f. is worth running the combined analysis. Chris

Re: [Freesurfer] nu_correct: Command not found error

I have encountered this error in the past, and I think it was because I was not sourcing SetUpFreeSurfer.sh correctly. That is the the script that sets up the MNI_DIR I think. echo $MNI_DIR or whatever it is called and it should show you if it is being setup properly. It may be pointing to the sy

[Freesurfer] long_qdec_table

Hey All, I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat using the following command: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat However, when I try and load it into QDEC afterwards I get the following error: Loading data

Re: [Freesurfer] long_qdec_table

are using and what > OS version, also the version of Python) > > Thanks, Martin > > > > On 03/13/2013 08:20 AM, Christopher McCarthy wrote: > > Hey All, > > I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat > using the following command: >

[Freesurfer] Expert file for recon-all -hires

Hi all, If I'm reading this < https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon> correctly, the current best practice for `-hires` is to include an expert file containing "mris_inflate -n 15", and that this should work for all voxel sizes (0.75mm)^3 - (1mm)^3? Or do we need to empirical

Re: [Freesurfer] Parallelization not working as implemented

Hello, I'd like to suggest an alternative, for anyone interested in going faster than 4 hours. I can't verify compatibility from a technical standpoint, but GNU Parallel (https://www.gnu.org/software/parallel/) has worked fast and run to completion reliably when batching multiple recon-all subj

[Freesurfer] Adjust bbregister affine to target raw T1

Hi all, Suppose you have a sub-pipeline: $ recon-all -s $SUBJ -i $T1 -all $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat --fslmat fsl.mat Now `bbreg.dat`/`fsl.mat` is registered to `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1? I've tried: $ tkregi

Re: [Freesurfer] Adjust bbregister affine to target raw T1

t fsl did not provide a good initial registration. If > you have v6, you can leave off --init-fsl and it will use mri_coreg > (which is more robust). > > > On 03/09/2017 03:24 PM, Christopher Markiewicz wrote: > > Hi all, > > > > Suppose you have a sub-pipeline: > >

[Freesurfer] BUG: bbregister --init-best needs to unset InitCoreg

Hi all, bbregister --init-best always produces "ERROR: cannot spec an init method with --init-best", because InitCoreg is defined as 1 by default, and never set to 0 by --init-best. (Setting something else that unsets InitCoreg will trigger the same error.) Example, given SUBJ and EPI: $ bbregis

Re: [Freesurfer] Adjust bbregister affine to target raw T1

I would not worry about some > being done with coreg and some with flirt > > On 3/9/17 3:40 PM, Christopher Markiewicz wrote: > > Hi Doug, > > This is the final line with "cost" in it: > > MinCost: 0.862331 7440.183178 7411.264107 -1.819400 > >

[Freesurfer] First-level GLM on externally-preprocessed functionals

Hi list, We're working on making a preprocessing stream that will be generally accessible to different analysis streams, including FreeSurfer. One component of this is sampling functional volumes to FreeSurfer meshes, and I want to test this component by running a simple first-level GLM in FreeSur

[Freesurfer] Survey on inputs for surface-based analysis pipelines

Hi list, We're working on FMRIPREP , a pipeline aimed at performing baseline preprocessing, and producing cleaned structural and functional data which can be fed into any of a number of analysis pipelines. We've recently begun incorporating surface r

[Freesurfer] mri_glmfit error (mri_reshape number of elements)

Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage surfaces, rather than self surfaces. I’ve already inspected the individual contrasts, loading the fsaverage surface in tksurfer and rendering ea

Re: [Freesurfer] negative header after preproc-sess

Hi Doug, I wonder if there's a plan to move to NIfTI-2 as the default encoding for .nii(.gz) images that would can't be encoded in a standard-conforming NIfTI-1? I believe all of the major packages support NIfTI-2 in their latest releases (with the possible exception of ANTs, which I don't beli

[Freesurfer] individual mri_segstats waveforms for vertices or face in label

Though one workaround might be to subdivide a label many, many times using mris_divide_parcellation, I was wondering if it is possible to obtain a per-vertex (or even per-face) fMRI waveform for a label. In other words, rather than compute the average waveform across all vertices, as with mri_se

[Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

Hi, I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs). The following produces a well-aligned output: mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii As does the following:

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

into translation, scale, and direction cosine, and then the matrix is thrown away. When a volume with the same geometry is written out, the matrix is recomputed. Some resolution is lost during the decomposition/recomposition, and we don't end up with the exact same matrix. On 10/14/17 1:30 PM, C

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

ave a special case (e.g. maybe we never tested registration across different resolutions or whatever?). Thanks, Martin https://gate.nmr.mgh.harvard.edu/filedrop2/ On 16. Oct 2017, at 19:37, Christopher Markiewicz mailto:markiew...@stanford.edu>> wrote: Doug, Sorry if I muddied things by goi

[Freesurfer] readVolGeom corner case leads to lta_convert failures

Hi all, We've run into an issue where lta_convert is failing if the filename line in a volume geometry is of a specific length. We've identified the source of the problem, and made a pull request on GitHub that at least partially fixes the issue (https://github.com/freesurfer/freesurfer/pull/18

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

d.edu on behalf of Christopher Markiewicz Sent: Tuesday, October 17, 2017 12:11:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms Hi Martin, I've uploaded a .tgz file with a T1w vo

[Freesurfer] recon-all on previously segmented volumes

Hi, I’m having some issues generating surfaces for an individual and was hoping that a combination of tools might help. In this particular individual, the skull stripping went fine, but a fairly large proportion of the anterior temporal cortex (primarily inferior) volume is excluded from the dat

[Freesurfer] RFC: Changes to nibabel API for .mgh/.mgz files

Hi all, I'd like to solicit input for the Python interface to .mgh/.mgz files in nibabel[0]. I've recently had cause to dig into this interface (MGHImage[1]), and found that the naming of header fields[2] (analogous to variable names in C structs) is inconsistent with all of my experience with

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

An epiphany lead me to the solution to the problem, which I shall post here since I am apparently due to experience it again in 2019. The NAN values in the GLM matrices were the result of there being a condition that did not appear in any of the .par files across all of the runs. Once these file

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