[Freesurfer] Fwd: [Neuroimaging] [Nibabel] Discourse category for Surface API discussions

External Email - Use Caution fyi -- Forwarded message - From: Christopher Markiewicz Date: Mon, Aug 9, 2021 at 5:01 PM Subject: [Neuroimaging] [Nibabel] Discourse category for Surface API discussions To: neuroimag...@python.org Hi all, I'm starting to work on

[Freesurfer] Pre SFN Workshop Nov 2-3, 2018: Hands-on Reproducible Analysis of Neuroimaging Data

External Email - Use Caution *Hands-on Reproducible Analysis of Neuroimaging Data* *A ReproNim Pre-SFN 2018 Training Workshop* *Register here: https://tinyurl.com/repronim-sfn18 * Purpose: An increasing body of evidence point to some issues in r

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

hi lea, in addition you could consider using the bids app for freesurfer: https://github.com/BIDS-Apps/freesurfer and then submit each subject's longitudinal pipeline as a separate slurm job. cheers, satra On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter wrote: > Hi Lea, > > > I wrote that sc

Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image

doing it, but there was no answer. I can > upload them to a Martinos file drop tomorrow morning if you want. > > Cheers, > Mel > > > On Oct 19, 2017 9:41 PM, Satrajit Ghosh wrote: > > hi sean, > > i think i ran those in june 2013 at ohbm. however, my recollection of

Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image

hi sean, i think i ran those in june 2013 at ohbm. however, my recollection of how it failed is encoded in that mail thread. it may be worthwhile to just run through those images with freesurfer 6.0. since it's only 6 brains, we can try running it through again. cheers, satra On Thu, Oct 19,

[Freesurfer] Repronim Training Workshop on Reproducible Research Nov 10-11 before SFN

*ReproNim Training Workshop: Nov 10 full day - Nov 11 morning - George Washington** University* *Register and information at:* ​https://tinyurl.com/repronim-sfn17 *Purpose:* The issue of lack of reproducibility has been described in several scientific domains for several years, raising concerns s

Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation

hi ruchira, while there is no freesurfer for windows, you can run freesurfer on windows using docker or vagrant or the windows subsystem for unix (windows 10 pro or better). i would recommend learning about these technologies first. probably the most useful at this point would be to learn about do

Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing

hi kirstie, this makes python 2 a requirement for freesurfer as distributed. i've started a PR that should at least help broaden the requirement to support python 2 and 3. https://github.com/freesurfer/freesurfer/pull/112 cheers, satra On Thu, Aug 3, 2017 at 3:41 AM, Kirstie Whitaker wrote:

[Freesurfer] Nipype Workshop and Hackweek at MIT, March 27-31, 2017

The Nipype development team will be holding a workshop and hackweek at MIT, Cambridge, MA, USA, from March 27 - 31. For details and registration see: http://nipy.org/workshops/ 2017-03-boston/index.html cheers, satra ___ Freesurfer mailing list Freesur

[Freesurfer] Open Neuroimaging Laboratory

Hi, The Open Neuroimaging Laboratory (http://openneu.ro) was one of the six finalists for the open science prize, and we presented our prototype platform at the NIH BD2K open science symposium on Dec 1. Check out our prototype for the #OpenSciencePrize and vote to help us advance in the finals! w

[Freesurfer] avoiding FSL when using T2pial

hi doug, without hacking recon-all is there a way to avoid using FSL when using the T2pial flag? cheers, satra #@# Refine Pial Surfs w/ T2/FLAIR Sat Sep 24 08:42:34 UTC 2016 bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-

Re: [Freesurfer] recon-all with input T1s at different resolutions

16 at 2:38 PM, Bruce Fischl wrote: > Hi Satra > > it will probably reject this by default, which you can get around be > reslicing one of them to be like the other. Or "conforming" both of them. > > cheers > Bruce > On > Tue, 31 May 2016, Satrajit Ghosh wrote:

[Freesurfer] recon-all with input T1s at different resolutions

hi folks, does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having). cheers, satra ___ Freesurfer mailing list Freesurfer@nm

[Freesurfer] Seeking postdoctoral candidates for datascience positions

science, electrical or biomedical engineering, neuroscience, statistics, or related field is required before starting this position. Positions are available for one year, with a possibility of yearly extension depending on performance and funding. For inquiries please contact Satrajit Ghosh (sa

[Freesurfer] reconstructing from T2 scan

hi bruce, we are missing a T1 scan from a participant. is there any pathway in freesurfer to reconstruct from the T2-flair/flash scan? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/lis

Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch

some posts about the minimum files required to run > recon-all, but I cannot find anything. Could you please try to find the > post in the archives and provide me the link? > > Thank you very much! > > > > Gesendet: Mittwoch, 19. November 2014 um 15:23 Uhr > Von: "Satr

Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch

hi jens, if you search the archives, there is a post that lists the minimal set of files needed for running recon-all. i used a tool called cde to create it: http://www.pgbovine.net/cde.html this reduces the archive down to about 650MB comprising binaries and atlases. this wouldn't be for gener

Re: [Freesurfer] Open MP parallel processing scaling factor?

hi andrew, i haven't done many systematic comparisons but there are a few practical considerations to take into account. in recon-all, i believe a few steps are affected by the openmp option and that creates resource underutilization. processors run idle when those steps are not being run. in my

Re: [Freesurfer] T2-space vs T2-space-FLAIR

; please don't count on the T2 and FLAIR options doing the same thing as I > suspect that they won't in the near future! > > > Bruce > On Wed, 30 Jul 2014, Satrajit Ghosh wrote: > > thanks matt, >> would like to be sure that your comments in relation to the T

Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks matt. cheers, satra On Wed, Jul 30, 2014 at 2:58 PM, Matt Glasser wrote: > Yes we performed both on the same subject in the same session and then > compared the myelin map results. > > Peace, > > Matt. > > From: Satrajit Ghosh > Reply-To: Freesurfer supp

Re: [Freesurfer] T2-space vs T2-space-FLAIR

(i.e. if myelin > maps were important to your study you might go with T2w (like HCP), but if > lesion detection were more important you might go with FLAIR (like > biobank). > > Peace, > > Matt. > > From: Satrajit Ghosh > Reply-To: Freesurfer support list >

[Freesurfer] T2-space vs T2-space-FLAIR

hi bruce, is there any difference from freesurfer's perspective of using T2-space or T2-space-flair? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] HBM Hackathon - please distribute widely !

The 2014 Hackathon registration is open! This unique 3-day event (June 5-7) will be held prior to annual meeting of the Organization for Human Bra

[Freesurfer] openmp/mkl support in tracula

hi a.y., is there any part of tracula that currently benefits from openmp or mkl availability? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] minimal data needed for maintaining edits

subjective, i'd like to provide those as part of data sharing). cheers, satra On Wed, Apr 16, 2014 at 5:16 PM, Satrajit Ghosh wrote: > hi, > > some of our freesurfer directories have become bloated with all kinds of > non-freesurfer data. if i want to rerun a subject in a n

[Freesurfer] minimal data needed for maintaining edits

hi, some of our freesurfer directories have become bloated with all kinds of non-freesurfer data. if i want to rerun a subject in a new location while maintaining the edits, is there a minimal list of files i should copy over? cheers, satra ___ Freesur

Re: [Freesurfer] tracula and libnetcdf

which, is there a patch (a 5.3.1) in the horizon which will include the tracula updates and perhaps netcdf in the freesurfer download. cheers, satra On Wed, Feb 5, 2014 at 11:07 PM, Satrajit Ghosh wrote: > update: the lack of libnetcdf eventually makes it fail. > > i found a libnetcd

[Freesurfer] Request for feedback on challenges/hurdles to using/learning Nipype

hi all, we are looking for feedback on learning/using/installing Nipype - any challenge or hurdle that may have derailed you, wasted your time, left you wanting a photon torpedo, etc.,. we are in the process of re-architecting components of Nipype and feedback would help a lot. please post/discu

Re: [Freesurfer] tracula and libnetcdf

update: the lack of libnetcdf eventually makes it fail. i found a libnetcdf.so.7 on the cluster and soft linked it to libnetcdf.so.6 and added the path to LD_LIBRARY_PATH. that let trac-all -prep run to completion. cheers, satra On Wed, Feb 5, 2014 at 9:02 PM, Satrajit Ghosh wrote: >

[Freesurfer] tracula and libnetcdf

hi a.y., when running trac-preproc i'm getting this error (for dmri_motion and dmri_group), but it continues running: /software/freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory what will this fail to do?

[Freesurfer] GPU considerations

Does Freesurfer's GPU bits care about single or double precision? Cheers, satra ___ 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 t

Re: [Freesurfer] Extract voxel time series from subcortical segmentation (without averaging)

hi martin, if you had one region you can use mri_segstats to extract for each voxel in that roi, but not for multiple rois. here is a snippet i use for timecourses in each roi. https://github.com/nipy/nipype/blob/master/examples/rsfmri_preprocessing.py#L219 cheers, satra On Tue, Nov 5, 2013

Re: [Freesurfer] new version of mri_segstats

is not a problem. If you run > recon-all partially, then it may fail because it runs mri_segstats before > the ribbon.mgz is created. > doug > > > > > On 11/04/2013 09:30 AM, Satrajit Ghosh wrote: > >> hi doug, >> >> could you please highlight the changes -

Re: [Freesurfer] new version of mri_segstats

hi doug, could you please highlight the changes - especially if there are any critical bug fixes? and should we rerun the new mri_segstats on our current 5.3 processed data? cheers, satra On Mon, Nov 4, 2013 at 9:26 AM, Douglas Greve wrote: > I've put new versions here: > ftp://surfer.nmr.mgh

Re: [Freesurfer] minimal freesurfer pieces for recon-all

, 2013 at 5:11 PM, Satrajit Ghosh wrote: > hi folks, > > has anybody on this list: > > a. built or extracted the necessary pieces (binaries, libraries, atlases) > for running vanilla recon-all only? > > b. or better still, has a package file for any linux distro? i know the

[Freesurfer] difference in atlas size

hi i noticed a big discrepancy in size between these two, but not among other lh and rh gcs files. > 28769857 May 13 17:21 rh.DKTatlas100.gcs > 6883965 May 13 17:21 lh.DKTatlas100.gcs are these the intended sizes? this is from the 5.3 centos6_x86_64 distro cheers, satra ___

[Freesurfer] minimal freesurfer pieces for recon-all

hi folks, has anybody on this list: a. built or extracted the necessary pieces (binaries, libraries, atlases) for running vanilla recon-all only? b. or better still, has a package file for any linux distro? i know the neurodebian folks are building one, but that's not fully ready yet. cheers,

Re: [Freesurfer] mri_vol2surf clarification

thanks very much doug. cheers, satra On Tue, Oct 8, 2013 at 11:55 AM, Douglas N Greve wrote: > > On 10/08/2013 09:17 AM, Satrajit Ghosh wrote: > > hi folks, > > > > i'm using mri_vol2surf to map functional time series into > > fsaverage3/4. my assumption is t

[Freesurfer] mri_vol2surf clarification

hi folks, i'm using mri_vol2surf to map functional time series into fsaverage3/4. my assumption is that each vertex time series will be the mean over an icosahedral patch corresponding to the vertex on fsaverage. is that how the resampling is done? also is the resampling done with a single interpo

Re: [Freesurfer] Freesurfer surface circle of pre-defined size

hi sarah, you'll get a much quicker response posting PySurfer related questions to: nipy-de...@neuroimaging.scipy.org cheers, satra On Fri, Jul 26, 2013 at 12:57 PM, wrote: > Hello Freesurfer Experts, > > We would like to use PySurfer's function plot_label_foci.py to > automatically create c

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

ayend...@nmr.mgh.harvard.edu> wrote: > > There is a *.thresh.label version of all the BA labels in 5.3, but I don't > think it's used by default. You can try using those labels instead. > > > On Fri, 26 Jul 2013, Satrajit Ghosh wrote: > > hi bruce, >> currently 5.3, but the

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

; version in 5.3, but perhaps she can comment. > Bruce > > On Fri, 26 Jul 2013, Satrajit Ghosh wrote: > > hi bruce, >> related to this question, how are the stats/volumes of the BAs computed? >> >> cheers, >> >> satra >> >> On Fri, Jul

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

hi bruce, related to this question, how are the stats/volumes of the BAs computed? cheers, satra On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl wrote: > Hi Laouchedi > > that is a big research question! The answer is a qualified yes, but it > depends strongly on what labels you mean. In general

Re: [Freesurfer] Loading thickness data in python

heers, satra On 15 July 2013 15:58, Satrajit Ghosh wrote: > >> hi sebastian, >> >> you simply need to read the geometry file and the morphometry vector and >> the two pieces will give you what you need. >> >> the geometry file gives you the relation

Re: [Freesurfer] Loading thickness data in python

hi sebastian, please take a look at pysurfer (https://github.com/nipy/pysurfer) and nibabel (https://github.com/nipy/nibabel). the relevant code is here: https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py cheers, satra On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs wrote:

Re: [Freesurfer] likelihood of identical subcortical volumes

Hi Satra > > this seems vanishingly unlikely to me, particularly with partial volume > correction. Have you visualize some of the subjects that have the same > structure volume? > > Bruce > > On Mon, 8 Jul 2013, Satrajit Ghosh wrote: > > a quick update. the followi

Re: [Freesurfer] likelihood of identical subcortical volumes

, 2013 at 1:07 PM, Satrajit Ghosh wrote: > hi, > > trying to figure out the likelihood of identical subcortical volumes > across individuals. i'm noticing this in some data processed with > FreeSurfer 5.1.0. > > just to give some probabilities - these are out of about 963 p

[Freesurfer] likelihood of identical subcortical volumes

hi, trying to figure out the likelihood of identical subcortical volumes across individuals. i'm noticing this in some data processed with FreeSurfer 5.1.0. just to give some probabilities - these are out of about 963 participants. and there are several such small clusters of identical numbers -

Re: [Freesurfer] T2pial refinement bbregister error

> On 07/05/2013 01:29 PM, Satrajit Ghosh wrote: > >> hi doug, >> >> same error with the updated one when i don't have FSL installed. >> >> writing to /data/subjects/H0351.2002/mri/**transforms/tmp.bbregister.** >> 7856/template.nii... >> fs

Re: [Freesurfer] T2pial refinement bbregister error

sch) then echo "ERROR: cannot find $FSLDIR/etc/flirtsch/xyztrans.sch" exit 1; endif endif ``` cheers, satra On Fri, Jul 5, 2013 at 1:05 PM, Satrajit Ghosh wrote: > thanks doug, i'll try that version right now. > > cheers, > > satra > >

Re: [Freesurfer] T2pial refinement bbregister error

version here > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister > > > > doug > > > On 07/05/2013 09:55 AM, Satrajit Ghosh wrote: > > hi doug, > > > > bbregister was running into an error trying to do T2pial refinement > > > >

Re: [Freesurfer] failure on 1 of the allen institute brains

ers > Bruce > > > On Fri, 5 Jul 2013, Satrajit Ghosh wrote: > > hi bruce and others: >> >> i'm getting a recon failure on this particular brain: H0351.1009 >> >> the quality isn't great, but if you can take a quick look at the brain to >>

[Freesurfer] T2pial refinement bbregister error

hi doug, bbregister was running into an error trying to do T2pial refinement sequence of commands and output here: https://gist.github.com/satra/5934639 and it looks like the absence of FSLDIR i didn't have FSL installed on this machine - i thought that freesurfer had it's own version of flirt

[Freesurfer] failure on 1 of the allen institute brains

hi bruce and others: i'm getting a recon failure on this particular brain: H0351.1009 the quality isn't great, but if you can take a quick look at the brain to see if you can spot any particular issues, that would be great. 4 of the others finished recon and 3 are almost there. cheers, satra

Re: [Freesurfer] [tracula] running into trouble with nifti data

e original Siemens gradients indicated. (Assuming the data > was acquired with the standard Siemens 60 gradient directions.) > > > a.y > > On Tue, 2 Jul 2013, Satrajit Ghosh wrote: > > hi ay, >> i'll look into the orientations a little later tonight, but

[Freesurfer] [tracula] running into trouble with nifti data

hi anastasia, i'm trying to debug a seg fault that some folks are seeing deep into a tracula run. process: 1. feed dicoms to a script that runs DTIPrep and outputs a nifti file, bvec, bval (among checking for many artifacts, this reduces the b=0 volumes to a single registered mean volume, runs

[Freesurfer] Technical Assistant Position Available at MIT

For details of the position and for applying see: http://sh.webhire.com/servlet/av/jd?ai=631&ji=2681168&sn=I ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

Re: [Freesurfer] Transform SMOOTHWM to DTI B0

hi dan, if you use bbregister to match the DTI b0 to freesurfer space, then you can transform the surface back (no guarantees on the tesselations though i think). the only additional component here would be a tkr transform that's based on the conformed space. i might even have some python code lyi

[Freesurfer] fsaverage mappings

hi folks, are there predefined mappings between the fsaverage surfaces? for example, i have an array of numbers for all the vertices in fsaverage4. is there an easy way to map those to vertices on to fsaverage/fsaverage5/... without going through surf2surf? something perhaps implemented in matlab

[Freesurfer] 5.2 ami

hi all, is there a public ami with freesurfer 5.2 available? cheers, satra ___ 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

Re: [Freesurfer] fsaverage across versions

> registration, or potentially elsewhere. I don't anticipate any large > changes, but I wouldn't count on them being identical > Bruce > > On Mon, 4 Feb 2013, Satrajit Ghosh wrote: > > hi bruce and others, >> are there any specific implications we should be worried

[Freesurfer] fsaverage across versions

hi bruce and others, are there any specific implications we should be worried about (e.g., with qdec or surf2surf) when using an fsaverage that's from a different version that ran the recon. cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.

Re: [Freesurfer] expected directory structure

h a thing. Maybe just run > recon-all and then ls -lR :) > doug > > > On 01/05/2013 02:48 PM, Satrajit Ghosh wrote: > > hi folks, > > > > happy new year. > > > > we are trying to create an object model for the freesurfer directory. > > > > is th

[Freesurfer] expected directory structure

hi folks, happy new year. we are trying to create an object model for the freesurfer directory. is there a function/script in freesurfer that would return me effectively something `ls -lR` but only the items that are mandatory for a subjects' directory? if not, is there a document that lists th

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

at to look at differences in myelin >>>> content, but I don't know all of the ways to calculate T1 or if you >>>> could >>>> get that from only two flip angles. Two images with roughly the same >>>> contrast won't work for the ratio method. You need to h

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

hi matt: could you generate the myelin maps say from two flash scans at different flip angles? bruce: if one had a choice between an mprage + t2 flair and 2 flash scans at 5/20 flip angles, what would be your recommendation? cheers, satra On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser wrote:

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

hi doug, just to follow up on this. if i had the phase encode direction (we currently store various dicom attributes in a nifti header extension), where would i provide it? cheers, satra On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve wrote: > Hi Clark, the phase encode direction is always

Re: [Freesurfer] subdividing consistently within aparc.annot

> Run program: > > mris_divide_parcellation mysubj001 rh aparc.annot splittable.txt > rh.aparc.split-sfg+pc > > This reads in rh.aparc.annot, splits the SFG and PC, and and saves the > result to rh.aparc.split-sfg+pc > > View > > tksurfer mysubj001 rh inflated -annot

Re: [Freesurfer] subdividing consistently within aparc.annot

. subj1: aparc.annot -> e.g i want to break up stg into 6 regions subj2: break up stg also into 6 regions such that there is a one to one correspondence between the subj2 regions and subj1 regions. cheers, satra > > Bruce > > On Wed, 3 Oct 2012, Satrajit Ghosh wrote: > > hi joh

Re: [Freesurfer] subdividing consistently within aparc.annot

n. cheers, satra On Wed, Oct 3, 2012 at 7:13 PM, John Griffiths wrote: > > > Would the Lausanne2008 template from the connectome mapping toolkit not do > the trick? > > > http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advanced.html > > > > On

[Freesurfer] subdividing consistently within aparc.annot

hi bruce, is there a way to divide consistently (same number of regions and one to one correspondence - obviously not the exact same areas) across subjects within aparc regions? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

[Freesurfer] fswiki down?

looks like the freesurfer wiki is down. cheers, satra ___ 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

Re: [Freesurfer] mri_surf2surf source and target annot formats

g the annot into a > segmentation (mris_annotation2label), passing that to surf2surf with > --sval (and --mapmethod nnf), then converting the output back to an > annotation (mris_seg2annot). This is what happens internally. > doug > > > > On 05/25/2012 09:52 AM, Satrajit G

Re: [Freesurfer] mri_surf2surf source and target annot formats

hi doug, we are trying to figure out if for annot we *have to* use sval-annot or if there is a way to do it with sval? cheers, satra On Fri, May 25, 2012 at 9:46 AM, Douglas Greve wrote: > If the source is an annot, then you need to use --sval-annot Is this > causing a problem? > doug > > On

[Freesurfer] request for dicom sequences on phantoms

howdy brain imagers, we are trying to put together a vocabulary of DICOM terms and their definitions related to brain imaging. unfortunately, a lot of the useful info is often in private tags and these differ from sequence to sequence and from scanner to scanner. to help us get at these tags, thi

Re: [Freesurfer] mri_vol2surf failed, segmentation error

hi Qingyang, you can simply copy and paste the command line into the shell. cheers, satra On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve wrote: > Can you run it outside of the pipeline to assure that it is not a > pipeline issue? > doug > > On 03/18/2012 08:54 AM, Qingyang Li wrote: > > Hi

Re: [Freesurfer] [BUG] epidewarp.fsl

/brain.nii.gz Standard error: if: Badly formed number. Return code: 1 Interface EPIDeWarp failed to run. --- On Mon, Mar 26, 2012 at 10:39 AM, Douglas N Greve wrote: > what does it do? What is the terminal output? > > Satrajit Ghosh wrote: > >> epidewarp.fsl does not take non-integer smoo

[Freesurfer] [BUG] epidewarp.fsl

epidewarp.fsl does not take non-integer smoothing kernel sizes. cheers, satra ___ 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 t

Re: [Freesurfer] [freesurfer] Is there any way to get the image from Tksurfer with white background?

depending on what you are doing you could use PySurfer. cheers, satra On Mon, Mar 12, 2012 at 6:04 PM, Bruce Fischl wrote: > no, sorry > On Mon, 12 Mar 2012, zhang mingxia wrote: > > Hi dear freesurfer experts, >> I am making pictures for publication. The images saving from Tksurfer >> are bla

Re: [Freesurfer] Use bbregister parameters to transform to EPI geometry

ined by > bbregister, is there any way to use those transformation parameters to take > the function scans into a common space that retains the original voxel size? > > Michael > > > On Mon, Dec 19, 2011 at 1:34 PM, Satrajit Ghosh wrote: > >> hi michael, >>

Re: [Freesurfer] Use bbregister parameters to transform to EPI geometry

>>> Michael >>> >>> On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu>> >>> wrote: >>> >>>That may or may not do what you want. I think th

Re: [Freesurfer] Use bbregister parameters to transform to EPI geometry

hey mike, take a look at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr cheers, satra On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom wrote: > Hi Doug, > > Is it possible to use the bbregister parameters to resample a functional > image such that it is in register wit

[Freesurfer] surfaces and gifti

hi all, this command: mris_convert --combinesurfs lh.pial rh.pial pial.gii.gz resulted in lh.pial.gii.gz (the help says it should generate pial.gii.gz). a related question. once i have this gifti file how do i get annotations+curvature info also into the file? (the gifti schema supports this rig

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

hi nick, i really like pedro's idea of tracking through instance tracking as opposed to licenses. on a separate project we are setting up the ability to pull up as many instances as necessary and install whatever software environment that's needed to run your analysis. we'll try to ensure that eac

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

hi nolan, i think starcluster is a great way to create a cluster on aws. but for those wanting to create a single instance and install things on an ami without actually having a large ami, fabric might be a good option. fabric: http://docs.fabfile.org/en/1.3.2/index.html example: (another neurod

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

hi pedro, will this work with gpu instances as well? cheers, satra 2011/11/9 Pedro Paulo de Magalhães Oliveira Junior > Some weeks ago I was asked about a public image (AMI) to run in the Amazon > EC2 infrastructure > > If you want to use FreeSurfer in the EC2 infrastructure you can use this

[Freesurfer] graph of region neighborhood

hi folks, do you happen to have any tool/script that produces a graph of aparc region neighborhood? with perhaps the edge weight being the length of shared boundary. cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

Re: [Freesurfer] strange freeview issue

satra On Tue, Sep 27, 2011 at 8:40 PM, Satrajit Ghosh wrote: > hi, > > we are seeing a strange freeview issue at mit and just wanted to check if > anybody else has seen this. we are running natty narwhal (ubuntu 11.04). > > details here: > > https://github.com/gablab

Re: [Freesurfer] strange freeview issue

he freeview from 5.1.0 to your 5.0.0 > installation? you would need to copy: > > freesurfer/lib/qt > freesurfer/bin/freeview > freesurfer/bin/freeview.bin > freesurver/bin/qt_setup.csh > > n. > > > > On Tue, 2011-09-27 at 20:40 -0400, Satrajit Ghosh wrote: > >

[Freesurfer] strange freeview issue

hi, we are seeing a strange freeview issue at mit and just wanted to check if anybody else has seen this. we are running natty narwhal (ubuntu 11.04). details here: https://github.com/gablab/mindhive/issues/1 cheers, satra ___ Freesurfer mailing list

[Freesurfer] .img extension read as analyze even though hdr says nifti1

hi all, when a .img extension file is passed to freesurfer routines, it is read in as analyze even if the header says it's a nifti image. we have observed that this causes a left-right flip in some cases. since a .img cannot exist without a header to be meaningful, shouldn't the appropriate type b

Re: [Freesurfer] PySurfer - A package for visualizing surfaces

hi mike, In theory it could, as we use Nibabel for i/o and they support Gifti. > However, I have no data in Gifti format at the moment to work with, so > at the moment I would say we are Freesurfer specific. > freesurfer does support giftis. mris_convert --combinesurfs fsaverage/surf/lh.inflated

Re: [Freesurfer] re-running recon-all failing

update: node on cluster had failing memory chip! cheers, satra On Mon, Jul 18, 2011 at 4:16 PM, Satrajit Ghosh wrote: > hi all, > > i'm trying to rerun some subjects processed with 5.0 with 5.1 and am > getting the following error on all the subjects. > > simply execut

[Freesurfer] re-running recon-all failing

hi all, i'm trying to rerun some subjects processed with 5.0 with 5.1 and am getting the following error on all the subjects. simply executing recon-all -s subjid -all any ideas? cheers, satra -- unfolding failed - restoring original position 0750: dt=0.001250, r

[Freesurfer] Request for DICOMS

hi, if you have pointers to publicly available DICOM data or willing to share such data publicly from different scanners and acquisition sequences for structural, diffusion and functional data from human participants, please contact me off list. currently, the more varied the scanners and sequenc

[Freesurfer] recon-all parallel execution of hemi stages

it seems we could run lh/rh processing stages of recon-all in parallel. however, i think they will write to the same log files. is there a way to specify a different log-file prefix? are there any other common files that these hemisphere based operations write to? concurrent reading i'm assuming i

[Freesurfer] mri_convert dicom conversion

hi, mri_convert TrioTim/123456-10-1.dcm test.nii.gz will scan all files in the dicom directory to get at series 10. in the above scenario, i know that the files corresponding to the run are 123456-10-*.dcm. is there a way to leverage this information, so that it does not scan the entire directory

[Freesurfer] brainmask

if one wants to get at the brain only (similar to bet), is brainmask.mgz the best file to use? on some of our data, we are noticing a lot of eyeball. i presume one can use aseg as an alternative. is this more recommended than brainmask.mgz? also, is the total brain volume computation based on aseg

[Freesurfer] mri_convert resample

can i use mri_convert to resample a 4-d nifti volume? currently it appears to write out just one frame. cmdline used: mri_convert -vs 2 2 2 r234000-20-1_warped.nii r234000-20-1_warped_fsresample.nii the input volume has 51 timepoints the output vol has 1. would you recommend another, more appro

[Freesurfer] Bvecs and image orientation

This question was asked on the FSL list and I thought it would be pertinent on this list as well in relation to mri_convert. -- Forwarded message -- From: Saad Jbabdi The bvecs are supposed to be relative to the image grid. On 22 Sep 2009, at 13:34, Laura Mancini wrote: Dear a

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