Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

Re: [Freesurfer] recon-all on version 4.5
by Saad Ramadan 07 Apr '11

07 Apr '11

Hi Bruce, I found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Fixing Bad Output From the Talairach Registration FreeSurfer computes a linear Talairach transform contained in a 3x4 matrix in a file called talairach.xfm and is located in the <subject name>/mri/transforms directory. Under some circumstances, the alignment can *fail the automatic failure detection scheme* (-tal-check flag, which can be disabled via -notal-check). Indeed, when I run recon-all with -notal-check, I donot see: *#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 in recon-all-staus.log file any more. Does this mean I have to do the manual talairach registration every time I run my recon-all, as it is a time consuming process? Is there any thing (from an acquisition perspective or otherwise) to eliminate this problem? Thanks in advance. On Thu, Apr 7, 2011 at 12:27 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > but you don't know what else was running on the same node at the time, do > you? Can you lock the amount of memory you will need? I think to be safe you > want 3G, but maybe Nick can chime in > > > On Thu, 7 Apr 2011, Saad Ramadan wrote: > > Hi Bruce, >> >> it is a cluster here a Brigham and wouldnot expect it to be low on memory. >> When I run a shell: >> free -mt >> >> I get: >> >> >> total used free shared buffers >> cached >> Mem: 3950 2918 1031 0 163 1596 >> -/+ buffers/cache: 1158 2791 >> Swap: 3820 125 3694 >> Total: 7770 3044 4725 >> >> >> On Thu, Apr 7, 2011 at 10:52 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> >wrote: >> >> how much memory do you have in that machine? >>> >>> Bruce >>> >>> On Thu, 7 Apr 2011, Saad Ramadan wrote: >>> >>> Dear all, >>> >>>> >>>> >>>> I ran (on an isotropic MPRAGE ): >>>> >>>> recon-all -subject mysubject -i >>>> ./DICOM/test.25.1.2010.04.27.21.51.18.31250.14004670.IMA -autorecon-all >>>> >>>> which ran for few hours and then exited without a successful end as can >>>> be >>>> seen on log file below. >>>> >>>> >>>> Contents of *recon-all-status.log* are: >>>> >>>> Wed Apr 6 12:31:55 EDT 2011 >>>> #@# MotionCor Wed Apr 6 12:33:10 EDT 2011 >>>> #@# Nu Intensity Correction Wed Apr 6 12:33:40 EDT 2011 >>>> #@# Talairach Wed Apr 6 12:35:22 EDT 2011 >>>> *#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 >>>> *#@# Intensity Normalization Wed Apr 6 12:36:53 EDT 2011 >>>> #@# Skull Stripping Wed Apr 6 12:41:44 EDT 2011 >>>> #@# EM Registration Wed Apr 6 14:16:04 EDT 2011 >>>> #@# CA Normalize Wed Apr 6 15:18:54 EDT 2011 >>>> #@# CA Reg Wed Apr 6 15:22:59 EDT 2011 >>>> >>>> The last few lines of *recon-all.log* produces: >>>> >>>> 0091: dt=0.112000, rms=0.700 (-0.001%), neg=0, invalid=766 >>>> resetting metric properties... >>>> setting smoothness coefficient to 10.00 >>>> blurring input image with Gaussian with sigma=2.000... >>>> 0000: dt=0.000, rms=0.638, neg=0, invalid=766 >>>> 0092: dt=0.772947, rms=0.623 (2.335%), neg=0, invalid=766 >>>> 0093: dt=0.028000, rms=0.622 (0.145%), neg=0, invalid=766 >>>> 0094: dt=0.028000, rms=0.622 (-0.063%), neg=0, invalid=766 >>>> blurring input image with Gaussian with sigma=0.500... >>>> 0000: dt=0.000, rms=0.622, neg=0, invalid=766 >>>> >>>> >>>> Do you have any idea what is going wrong here? >>>> >>>> Thanks >>>> >>>> >>>> >>> 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 to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>

2 1

gcut
by Dougherty, Michael 07 Apr '11

07 Apr '11

Hello all, I would like to take advantage of the gcut feature to remove dura that gets included in many subjects in my dataset. I am using v5.0.0, but when i enter the command from the wiki: recon-all -skullstrip -clean-bm -gcut -subjid <subjid> , i get an exit recon-all with errors, saying "ERROR: Flag -gcut unrecognized." Any suggestions, so that I can avoid doing all of these edits manually? Michael

2 1

Slice Order
by Rita Loiotile 07 Apr '11

07 Apr '11

If my BOLD scan has 30 slices in "interleaved" series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30?

3 4

Clusterwise correction
by Irene Altarelli 07 Apr '11

07 Apr '11

Dear Freesurfers, I am doing a vertex-by-vertex analysis on a label, using mri_glmfit. As a result, I got a very small cluster (62 vertices) at p<0.01. Then I tried running clusterwise correction using the following command: mri_glmfit-sim \ --glmdir fMRIfaces20.glmdir \ --sim mc-z 5000 2 mc-z.pos \ --sim-sign pos \ --overwrite I am a bit surprised by the result: one cluster is reported in mc-z.pos.sig.cluster.summary, and it is bigger than the one previously identified. Could this be correct? if not, what could I be doing wrong? Please find attached mc-z.pos.sig.cluster.summary and mc-z.pos.j001-lh-try-ctr-dys2.csd. Thanks very much in advance, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23

2 1

vidualizing fcseed results
by Y.V. Jiang 07 Apr '11

07 Apr '11

Hi Doug, I ran fcseed-sess in Freesurfer 5.1, all the way through selxavg3-sess. How can the results be visualized, given that no contrast was specified? In the freesurfer wiki, it is said that "a contrast does not need to be made because one is automatically created with an -taskreg". But without a contrast I am not sure what the data can be visualized?? Thank you. -Yuhong

2 1

recon-all on version 4.5
by Saad Ramadan 07 Apr '11

07 Apr '11

Dear all, I ran (on an isotropic MPRAGE ): recon-all -subject mysubject -i ./DICOM/test.25.1.2010.04.27.21.51.18.31250.14004670.IMA -autorecon-all which ran for few hours and then exited without a successful end as can be seen on log file below. Contents of *recon-all-status.log* are: Wed Apr 6 12:31:55 EDT 2011 #@# MotionCor Wed Apr 6 12:33:10 EDT 2011 #@# Nu Intensity Correction Wed Apr 6 12:33:40 EDT 2011 #@# Talairach Wed Apr 6 12:35:22 EDT 2011 *#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 *#@# Intensity Normalization Wed Apr 6 12:36:53 EDT 2011 #@# Skull Stripping Wed Apr 6 12:41:44 EDT 2011 #@# EM Registration Wed Apr 6 14:16:04 EDT 2011 #@# CA Normalize Wed Apr 6 15:18:54 EDT 2011 #@# CA Reg Wed Apr 6 15:22:59 EDT 2011 The last few lines of *recon-all.log* produces: 0091: dt=0.112000, rms=0.700 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 0092: dt=0.772947, rms=0.623 (2.335%), neg=0, invalid=766 0093: dt=0.028000, rms=0.622 (0.145%), neg=0, invalid=766 0094: dt=0.028000, rms=0.622 (-0.063%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=766 Do you have any idea what is going wrong here? Thanks

3 2

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

4 4

the threshold value in qdec window
by 汪贵宏 07 Apr '11

07 Apr '11

Hi all, I used the freesurfer 5.0,there is a question in my reseach,may be not a question! When i view the results of analysis in the qdec window,why did i cannot change the value of the Threshold,such as min(which had been seted with the value of 2) ,in the same way,the max is 5?If i want to change the value of them,how can i do it? thanks a lot wang

1 0

wmparc
by Jose Soares 06 Apr '11

06 Apr '11

Hi all, I am working with FS 4.5 and 5.0 and I have noticed that in wmparc.stats in 5.0 there are volumes (segmentations) that do not appear in the wmparc.stats file (and appear in 4.5 version), for instance the subcortical structures, ventricles, cerebellum. In wmparc V 4.5 I have 1189 rows with structures and in v 5.0 I just have 70. Why is this? Thanks for the help, Jose.

2 1

Freesurfer visuliazation
by Ritobrato Datta 06 Apr '11

06 Apr '11

Hello All, I have two questions. 1. Is there a way to save a vtk format WITH greyscale gyri/sulci outlines ? 2. Is there a way to modify the color spectrum with the viewer? I am trying to get a gradient like attached, but am having extreme trouble obtaining it. Thanks Ri

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Freesurfer April 2011