[Freesurfer] error message recon-all

.dcm 74.dcm 80.dcm 87.dcm 93.dcm 9.dcm 106.dcm 112.dcm 119.dcm 125.dcm 131.dcm 138.dcm 144.dcm 150.dcm 157.dcm 18.dcm 24.dcm 30.dcm 37.dcm 43.dcm 4.dcm 56.dcm 62.dcm 69.dcm 75.dcm 81.dcm 88.dcm 94.dcm yours, Lars M. Rimol, PhD Norwegian University of Science and

[Freesurfer] Tracula reinit

er to have a larger number of control points, except for the increase (I assume) in processing time? Or will a larger number produce a worse result for less curved tracts? yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, N

[Freesurfer] recon-all

? I'm unsure if 060027_S01_to_060027.lta is supposed to be there before mri_robust_template starts? Is that the problem or is it something else? Any help would be appreciated, Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTN

[Freesurfer] configure overlay display in tksurfer by keyboard inputs

yours, Lars M. Rimol, PhD Department of Medicine John A. Burns School of Medicine University of Hawai'i 1356 Lusitana Street, University Tower Honolulu, HI 96813 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harv

[Freesurfer] visualizing statistical maps in FreeView

Hi, Is it possible to overlay .mgh files with statistics (e.g. p-maps) directly in FreeView, for purposes of visualizing the results, the same way you can in tksurfer? When I try load an overlay in FreeView, it seems to be expecting a volume file. Thank you! sincerely yours, Lars M. Rimol

[Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars

Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

t get generated look fine too? a.y On Sat, 2 Jul 2016, Lars M. Rimol wrote: Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of row

[Freesurfer] Tracula movement

HI, Is there a rule-of-thumb upper level of acceptable head motion? The tutorial gives these values as examples: AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 0.489419 0.00398925 0 1 I have a subject with AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore *30.018* 0.209

[Freesurfer] trac-all -path Segmentation fault

+0200 2016 Where do I go next? sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ Freesurfer mailing

[Freesurfer] tracula reinit

Hi, Rerunning the tractography using reinit, is it an absolute requirement to specify number of control points? It doesn't seem like I can just set reinit = 1 and let the number of control points be the default. Also, is there a trade-off in terms of number of control points? For instance, when re

Re: [Freesurfer] tracula reinit

reasing the >control points in general, it depends on the specific case. >BTW, if you change the number of control points, you don't need to use the >reinit variable - that's only for rerunning with the same control points >as before. > >Best, >a.y sincerely yours,

[Freesurfer] Error in load_mgh

string constant. Error in load_mgh (line 158) switch type (PS! I've tried chancing the file name to just lh.mgh but get the same error message. And the file(s) exist and the path is correct.) sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functio

[Freesurfer] failure to start tksurfer

x27;t create a context! surfer: failed, trying double buffered window Received X error! Error code : 2 Request code : 154 Minor code : 3 Error text : 'BadValue (integer parameter out of range for operation)' Can't create a context! surfer: failed, no suitable disp

[Freesurfer] if: Expression Syntax.

urs, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harv

[Freesurfer] mris_preproc on zipped data

rely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] errors message in QAtools

Apart from this, the snapshots look ok (except for one subject I asked about in a previous e-mail) and there are no outliers in any of the subjects (according to QAtools). Any idea why I get this error message? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Adviso

[Freesurfer] asegstats2table list index out of range

#x27; names individually. With over 100 subjects, however, that's not an option. I'd be grateful for any suggestion on how to run asegstats2table with a subjects list. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Depart

[Freesurfer] Image geometries differ across time

0 0. 0. 1. sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ Freesurfer mailing list Freesurfer@n

[Freesurfer] FLIRT in Han et al., 2006

n et al., 2002). The volumetric registration matrix is then applied to the corresponding surfaces." Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University ho

[Freesurfer] Per-vertex regressors

fy voxel-specific regressors to append to the design matrix. Note: the contrast matrices must include columns for these components. Thank you! -- yours, Lars M. Rimol, PhD Division of Mental Health and Addiction Institute of Clinical Medicine University of Osl

[Freesurfer] problems with recon-all in 6.0

hy it crashes, and why does it add "?" to the subject name? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 70

[Freesurfer] problem with bedpostx

ep on a cluster bedpostx_mgh -n 2 /home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local/1001_c1/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected Sincerely yours, Lars M. Rimol, PhD Senior Researcher Norwegian Advisor

[Freesurfer] longitudinal TRACULA

16-32.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any idea what went wrong here? Thank you! Sincerely yours, Lars M. Rimol, PhD Senior Researcher Norwegian Advisory Unit for Functional MRI Department of Radiology St. Olav's Univer

[Freesurfer] problems with cortical surface area maps

Hi Anderson, Thank you! How would you suggest I address this issue when I smooth these images before statistical analysis? I normally use the smoothing algorithm implemented in FreeSurfer (mri_surf2surf). -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

Re: [Freesurfer] Linear Mixed Models in FS?

ly equal to the coefficient of the time covariate (the second covariate) when the group covariate is zero (i.e for the controls). Hope this makes sense. Best -Jorge -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing

[Freesurfer] create label from binary .mgh file

, but that seems to produce volumes and I'm not really sure what it does anyway... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

Re: [Freesurfer] Correlation coeffecient

link within this post is dead? > > any help is greatly appreciated > > thanks, > Chris -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.

Re: [Freesurfer] create label from binary .mgh file {Disarmed}

surfer@nmr.mgh.harvard.edu&q=date:20140711> use mri_cor2label with the --surf option On 07/11/2014 01:36 PM, Bruce Fischl wrote: > Hi Lars > > this would be pretty simple to do in matlab, but I'm not sure if we > have anything do to it otherwise (Doug might) > > cheers &

Re: [Freesurfer] mri_cor2label revisited

ce/tanha_002/users/greve/fsdev.build/lib/tcl/ > fsgdfPlot.tcl > Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/ > tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > > > > > On 07/15/2014 09:04 AM, Lars M. Rimol wrote

[Freesurfer] proportion of surface area of significant region

s changed by both the topology correction and the surface deformation. Note that the fsaverage surface area is less than any individual subject due to smoothing of the surface, which is why we include a correction factor in the fsaverage surfaces. cheers, Bruce On Wed, 16 Sep 2009, Lars M. Rimol

Re: [Freesurfer] proportion of surface area of significant region

is is the average of the group used to create fsaverage), or, probably better, get an average area map for your cohort doug On 07/30/2014 08:38 AM, Lars M. Rimol wrote: > Hi Bruce, > > I would like to be able to tell what proportion of a region of > interest (ROI), as defined in atlas spac

[Freesurfer] how to interpret a change in area of 0.004 mm² per year?

this Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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 onl

[Freesurfer] problem with mris_preproc

.(null) No such file or directory ERROR: reading curvature file -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

[Freesurfer] lgi mris_preproc

lh.pial_lgi To perform a vertex-wise analysis in QDEC of the lgi surface data, first sample the results to the average template subject 'fsaverage': recon-all -s my_subject_id -qcache -measure pial_lgi Do this for each of the subjects in your group -- yours, Lars M. Rimol, PhD Norwegian

Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?

Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in thi

Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?

lme assumes a normal distribution and it's unclear to me what the distribution of such ratios are. Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway > Bruce Fischl > <http://www.mail-archive.com/search?l=freesurfer@n

Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?

Hi Martin, Does that mean that one would expect to see reduced lgi (local gyrification index) where this occurs? Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway On Wed, Oct 29, 2014 at 3:39 PM, Martin Reuter wrote: >

[Freesurfer] white matter snr

documented.) Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Fwd: comparing lme models

ors I can drop from the covariance model? Have I understood you correctly? Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway On Wed, Dec 17, 2014 at 5:00 PM, jorge luis wrote: > > Hi Lars > > I'm not sure whether

[Freesurfer] freeglut ERROR

Hi, In tksurfer, when I have loaded an overlay and then try to add a color bar, I get this error message: freeglut ERROR: Function called without first calling 'glutInit' I'm using freeglut v 2.4.0. I don't know if this is caused by a bug in freeglut (I think it's the latest version). Anyone kno

[Freesurfer] getting vertex numbers

Hi, I've done a glm model fit comparing cortical thickness between two groups, and have certain areas ("blobs") on the cortical surface that are above sig. threshold. I'd like to get a list of the vertex numbers for each of these significant areas, which do not correspond to the parcellations in FS

[Freesurfer] standard error for betas

Hi, I have fitted a glm with three different groups, using mri_glmfit (FS v4.0.3). I use the beta.mgh to get the adjusted means within an ROI, for each group. I'd like to make a bar or box diagram with the adjusted means/betas, but I'm not sure how to get the standard error of the betas so I can ma

[Freesurfer] effect sizes and SE

Hi, Is there a way to get the standard error of the adjusted means for each group in a glm with a categorical predictor? -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

RE: [Freesurfer] Destrieux or Desikan/Ron Killiany

> cheers, > Bruce > On Tue, 10 Mar 2009, Lars M. Rimol wrote: > > > Hi, > > I have an area of significance on the mesial surface of the hemisphere > > (please see attached tiffs). I would like to know if it is exclusively in > > the cingulate or in cingulate

RE: [Freesurfer] Destrieux or Desikan/Ron Killiany

Hi Rahul, Thanks for the input! I'm afraid I don't see how the atlases agree with regard to the medial SFG, since only a tiny portion of the area of interest is in SFG according to the Destriuex annotation (SFG is the uppermost parcellation in the anterior half of the hemisphere in that i

[Freesurfer] homologous lh and rh labels

Hi, This is perhaps a tricky problem. I have created a lh STG label using "custom fill" and the "up to functional threshold" option and retrieved the data from those vertices. This label is just a minor portion of the entire STG parcellation. Now I would like to compare to the homologous area in th

[Freesurfer] FDR correction

Hi, I have done an analysis involving three groups, so there are three pairwise comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple comparisons (across the vertices), so I use FDR. But since FDR determines the threshold basd on the actual p-values, I get 6 different treshol

RE: [Freesurfer] FDR correction

at 12:38, Lars M. Rimol wrote: Hi, I have done an analysis involving three groups, so there are three pairwise comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple comparisons (across the vertices), so I use FDR. But since FDR determines the threshold basd on the actual p-

Re: [Freesurfer] FDR correction

ue everywhere, you are controlling FWE, even using an FDR > procedure) for each comparison if the null for any of these comparisons is > true everywhere. > > This also means that, although FDR would still be controlled globally, one > cannot make inferences about each comparison indivi

[Freesurfer] fdr thresholds in tksurfer compared to Nichol's function

Hi, I've used the fdr function in tksurfer and compared the results to Tom Nichol's matlab function (http://www.sph.umich.edu/~nichols/FDR/). I use p = 10.^-abs(pfile), where "pfile" is 'sig.mgh'. I find that the p-threshold (pID, assuming positive dependence) is usually exactly the sam

[Freesurfer] RE: fdr thresholds in tksurfer compared to Nichol's function

Hi, Please disregard my previous mail. I was a little too trigger happy..., the 1.928 threshold set by tksurfer is too high for any vertex to survive so the two methods DO concur. I should actually look at the maps and not just the output... The reason I asked is that I'm combining i

RE: [Fwd: Re: [Freesurfer] setting of fdr thresholds in qdec]

Mike (and Jorge), Thanks! yours, LMR > Subject: [Fwd: Re: [Freesurfer] setting of fdr thresholds in qdec] > From: mha...@conte.wustl.edu > To: freesurfer@nmr.mgh.harvard.edu; lari...@gmail.com > Date: Thu, 25 Jun 2009 10:08:05 -0500 > > > Lars, > I had a similar question regard

[Freesurfer] cannot read file as type 3

Hi, What does it mean when mris_surf2surf produces the error message that the input file cannot be read "as type 3" ? The file is an .mgh which I converted from an .mgz using mri_convert (mri_convert oldfile.mgz newfile.mgh). I get the same error when I use the .mgz file. Thank yo

RE: [Freesurfer] cannot read file as type 3

Yes, I can load it as an overlay in tksurfer. Here's the mri_info output: [...@localhost area]$ mri_info TOP_sm100_lh_cc2_11072009.mgh Volume information for TOP_sm100_lh_cc2_11072009.mgh type: MGH dimensions: 163842 x 1 x 1 x 216 voxel sizes: 1., 1., 1. type: FLOAT (3) f

RE: [Freesurfer] cannot read file as type 3

i...@gmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] cannot read file as type 3 > > Hi Lars, > > can you send us the whole command line and output? I think type 3 is an > MGH/MGZ file. Does mri_info work on it properly? > > cheers > Br

[Freesurfer] FW: questions about the surface processing stream

flect average brain size.) Is that correct? And does this mean that the size of the faces/triangles is uniform across all locations and subjects, at least before the topology fix? Thank you! Lars M. Rimol ___ Freesurfer mailing list Frees

[Freesurfer] CEPHES ERROR: fdtrc domain error

two groups, and age and ICV as continuous regressors. The error message comes when estimating the 0 0 0 1 contrast, i.e. ICV. Matrix condition = 494.18. The beta for this covariate shows very small numbers, i.e. 0-6*10^-1. And the sig.mgh file for it shows all vertices = 1e+10. yours,

[Freesurfer] optic nerve

Dear all, Do you recomend to routinely erase the optic nerve (regardless of how the wm surface looks), and where in the work flow do you recomend to do it? (We do it as part of the quality control after autorecon1 now.)-- yours,LMR ___ Freesurfer mailin

[Freesurfer] which script creates the design matrix?

Hi, I am using FS v3.02. I am using the tutorial to figure out how to do group analysis with the new FS version but there is one step that is confusing. The tutorial says that I should first create a FSGDF (and run make_average-subject), and then it says that running mris_glm will create the design

[Freesurfer] problems with group analysis (mri_glmfit?)

Hi, I did a group analysis on 10 subjects (as a test run) following the steps of the updated tutorial. I get no error messages, however, when I load the y.fsgd, there are no data points. These 10 subjects were chosen randomly, solely for the purpose of running through the group analysis procedure,

[Freesurfer] statistics without mri_glmfit

Hi, I would like to analyse my data without using the mri_glmfit, because it is not flexible enough for my current purposes. But I would like to use mris_preproc and surf2surf in order to get the data into common space. However, when executing the mris_preproc I am required to specify a FSGD file,

[Freesurfer] make_average_subject

Hi, I have two questions on make_average_subject1) Why are two sets of surfaces created by the make_average_subjectscript? What is the difference between e.g. inflated and inflated_avg?Which one(s) should be used for visualization? 2) As far as I understand, make_average_subject is run for visualiz

[Freesurfer] problems with make_average_subject

Hi, I am analysing a dataset with 180 subjects. When I run make_average_subjects it crashes, the error message usually being something like this: mghRead: encountered error executing: 'zcat /space/monkeys/1/home/lmr/subjects/VETSA_test/testAVG/tmp/make_average_vol-tmp/orig-19963b.mgz',frame -1 I

[Freesurfer] make_average_subject memory issues

Hi, I just ran make_average_subjects with increased swap (from 2G to 8G) on 178 subjects and now it worked, which would seem to indicate that it may have been a memory issue? I did not crash with 3, 10 and 113 subjects with 2G swap. yours, LMR >Hmmm, I've run it on >100 subjects without trouble.

[Freesurfer] smoothing

Hi, In the --help output of mri_surf2surf, the following explanation is given for --fwhm-src fwhmsrc:     Smooth the source or target with a gaussian with the given fwhm (mm). This is     actually an approximation done using iterative nearest neighbor smoothing.     The number of iterations is com

[Freesurfer] questions about group analysis

Hi, I have three questions: 1) Where can I find information on what the different output files of mri_glmfit represent, i.e. ar1.mgh eres.mgh rstd.mgh rvar.mgh These can all be plotted (Load Overlay) since they are .mgh files but they seem to rarely show any blobs (except with extremely liberal th

[Freesurfer] source of thickness information for mris_preproc

Hi, When one runs mris_preproc with e.g. -meas thickness, does it get the thickness information from the files in the stats directory within each subject's directory - or from the ?h.thickness files under the surf directories?   Thank you!-- yours,LMR

[Freesurfer] output from single subject sphere morph to atlas

Hi, Is the determinant of the Jacobian matrix for the sphere morph to atlas space saved vertex by vertex? If so, where is it saved? -- yours,LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/

[Freesurfer] mri_concat

Hi, I am wondering if it is possible to use some kind of a list of subjects to specify input for mri_concat, like you can use --f filename, where filename refers to a list of subjects, for mri_surf2surf ? It seems that using e.g.: mri_concat subj*-lh.mgz --o allsubjs-lh.mgz is an alternative to:

[Freesurfer] mris_preproc

Hi, When I try to run mris_preproc wiht the nocleanup flag I get an error message: flag --nocleanup not recognized Same thing happens for --cleanup (i.e., not recognized), and "--tmpdir tmpdir" doesn't seem to work (it still does cleanup). But all these flags are listed under the help function fo

[Freesurfer] smoothing with mris_preproc

Hi, If I don't specify any smoothing level when running mris_preproc, with --fwhm or --niters, does that mean that it won't apply any smoothing or is there a default smoothing level? -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

[Freesurfer] color coding for parcellations/regions of interest

Hi, I have combined the Desikan parcellations into regions of interest, which I would like to visualize. So I need to create an ad hoc color coding scheme. In order to visualize the ROIs I would load a file equivalent to the ?h.aparca2005s.annot file, which would show the same color for those parc

[Freesurfer] make_average-subject

Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v

[Freesurfer] make_average_subject

f the subjectsdir, and also write the output to that dir? It seems if you give the full path, FS assumes that it should be added to the path of the subjects dir. Thank you! Lars Hi Lars, it looks like no input subjects are defined. Bruce On Wed, 27 Jun 2007, Lars M. Rimol wrote: Hi, Trying t

[Freesurfer] mri_glmfit

Hi, I ran mri_glmfit with a fsgdf looking (in principle) like this: GroupDescriptorFile 1 Title MyTitle Class Group1 plus blue Class Group2 circle green Variables ICV Input subjid1 Group1 1 Input subjid2 Group22 Dependent variable iscortical thickness. When I "lo

[Freesurfer] mri_glmfit

Hi, Please ignore my previous mail, I did not see that "external" on the y axis means dependent variable (blame it on the early morning blues...) -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

[Freesurfer] installation

Hi, I downloaded the freesurfer-Linux-rh9-stable-pub-v4.0.3-full, and I followed the instructions on your website ( http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-platform-release-full.README.txt ): 1) extract to /usr/pubsw/packages/ 2) place the license file in the resulting /usr/pubs

[Freesurfer] imensions of an mgh file generated by

Hi, I'm just wondering what the dimensions of an mgh file generated by mris_preproc with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I would assume that it should contain a vector for each vertex, with the same length as number of subjects that were listed in the fsgd file u

[Freesurfer] Dimensions of an mgh file generated by mris_preproc

Hi, I'm wondering what the dimensions of an mgh file generated by mris_preproc with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I would assume that it should contain a vector for each vertex, with the same length as number of subjects that were listed in the fsgd file used wi

[Freesurfer] freesurfer version 3.0 ?

Hi, We have a dataset that was processed (by somebody else) with an old freesurfer version and we need to find out exactly which version was used. We have a freesurfer_3.0 directory (and a freesurfer-Linux-centos4-stable-v3.0-full.tar.gz download) with a build-stamp.txt that says: freesurfer-Linux-

[Freesurfer] tksurfer problems

Hi, I am experiencing similar problems to Jennifer and Glenn with tksurfer; the (tksurfer) error message is: surfer: ### redraw failed: no gl window open and the display shows only a thin slice of the posterior of the surface. The computer is a fresh install of RHEL 5 on a new machine, and my

[Freesurfer] corpus callosum coordinates

any way to get this info from the data recon'ed with v3.0.2? Thank you! yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail i

[Freesurfer] error message in mri_concat: fp==0

-- yours, Dr. Lars M. Rimol ___ 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

Re: [Freesurfer] error message in mri_concat: fp==0

Fischl wrote: > Hi Lars > > do you have write permission? Is the partition full? Try: > > touch /home/lmr/test.mgh > > and see if that works > > cheers > Bruce > > > > > On Thu, 20 Jan > 2011, Lars M. Rimol wrote: > >> Hi, >> >>

Re: [Freesurfer] error message in mri_concat: fp==0

gt; what does it tell you? > > On Thu, 20 Jan 2011, > Lars M. Rimol wrote: > >> Hi Bruce, >> >> Yes I can create files. I was trying to run a script with almost 500 >> mgh files that I wanted to concatenate. I figured there was something >> wrong with the scr

Re: [Freesurfer] error message in mri_concat: fp==0

stacksize 10240 kbytes, sorry! -- yours, Dr. Lars M. Rimol ___ 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

[Freesurfer] residuals exactly zero

. Is this correctly understood? Is this also the case in the underlying C-code? Thank you! LMR -- yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] Cerebellum atlas

, Sedvall G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7)-- yours, Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] talairach transform with brain.mgz as input file

urs,Lars M. Rimol  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] talairach transform with brain.mgz

tive Value improves, that's why we've started using that. So we need to know how to proceed from there.(We use the "recommended reconstruction," so we check the talairach and skullstrip after autorecon1.)   Thanks! -- yours,Lars M. Rimol   >depends why you needed to improv

[Freesurfer] cerebellum segmentation

gray and>white. I guess it's a question of what your goals are Lars.-- yours,Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer