Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

handles in the non-cortical regions, does it matter?
by xuemei lei 21 Nov '10

21 Nov '10

Hi, I have ran the recon-all, and got some handls in the non-cortical regions caused by the islands in C140-150 slices, and I am just interested in the cortical regions. I don't want to fix it. I want to know whether it matters or not。 Thank you for help -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning<http://psychbrain.bnu.edu.cn> Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 ============================================== Welcome to visit my blog: www.mobiye.com

2 2

handles in the non-cortical regions, does it matter?
by xuemei lei 21 Nov '10

21 Nov '10

1 0

qcache
by Dhinakaran Chinappen 20 Nov '10

20 Nov '10

Dear Freesurfer(ers). Quick ques: is it possible to run recon-all with the qcache flag during the initial reconstruction, as opposed to re-using recon-all with the qcache flag afterwards? Thanks, Dhinakaran.

2 1

Re: [Freesurfer] volumetry of PSP related structures...
by a.cerasa＠isn.cnr.it 20 Nov '10

20 Nov '10

Dear Gonzalo We've a PSP-freesufer paper in revision on Parkinsonisms and Related Disorders. In this particular population FS confirms evidence provided by previous VBM studies. ----- Original Message ----- From: Gonzalo Rojas Costa To: freesurfer(a)nmr.mgh.harvard.edu Sent: Fri, 19 Nov 2010 18:14:38 -0300 Subject: [Freesurfer] volumetry of PSP related structures... Hi: How can I get the volume of pons, middle cerebellar pedunclues, superior cerebellar peduncles ?... And, there exist any PSP-Freesurfer related paper ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl _______________________________________________ Freesurfer mailing list Freesurfer(a)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 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. -- This message was scanned by ESVA and is believed to be clean. Click here to report this message as spam. http://smtp.isn.cnr.it/cgi-bin/learn-msg.cgi?id=5B9DE28046.8BE5A

1 0

recon1: brain missing
by suzanne oosterwijk 19 Nov '10

19 Nov '10

Hi, I have been running recon1 recently and I have noticed that for some of my participants big chunks are missing in the brainmask.mgz. Out of 20 participants, five participants have this problem. The pattern is similar across participants: the missing parts start around slice 70-50 at the bottom (cerebellum) and then move upward. The data can be found in: /autofs/space/boggart_001/users/oosterwi/construct_struc It concerns constr011 (which I corrected using the clone method), and constr012, constr016, constr019 and constr020 (which still show the problem). I think it can be solved by cloning the T1 (aux volume) as is explained in the Freesurfer tutorial. Still, I wonder whether this is the best solution, and why this is happening in the first place. I appreciate any help or feedback on this. Thanks in advance! kind regards, Suzanne Oosterwijk -- Suzanne Oosterwijk Postdoctoral Researcher Interdisciplinary Affective Science Lab Department of Psychology Northeastern University 114 Lake Hall s.oosterwijk(a)neu.edu

2 1

volumetry of PSP related structures...
by Gonzalo Rojas Costa 19 Nov '10

19 Nov '10

Hi: How can I get the volume of pons, middle cerebellar pedunclues, superior cerebellar peduncles ?... And, there exist any PSP-Freesurfer related paper ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 1

Re: [Freesurfer] freeview load overlay error...
by Gonzalo Rojas Costa 19 Nov '10

19 Nov '10

Dear Dr. Wang: I got the message: "mris_info zstat3_rh.w nquads=8321536, nvertices=2 ERROR: MRISread: file 'zstat3_rh.w' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory" Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 18-11-2010 15:57, Gonzalo Rojas escribió: > Message: 4 > Date: Mon, 15 Nov 2010 09:36:17 -0500 > From: Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] freeview load overlay error... > To: freesurfer(a)nmr.mgh.harvard.edu > > What does mris_info show on the overlay file? > > On 11/14/10 11:08 PM, Gonzalo Rojas Costa wrote: >> Hi: >> >> I generated a surface with: >> >> mri_vol2surf --src zstat3.nii.gz --src_type nifti --srcreg >> ../registro.dat >> --hemi lh --projfrac 0.5 --out ./zstat3_lh.w --out_type w >> >> then I tried to load zstat3_lh.w using freeview, but I got the error: >> >> "MRISreadBinaryCurvature: incompatible vertex number in file >> /home/gonzalorojas/Desktop/rendering_broca_wernicke_paper/diestroBL_cov/zstat3_lh.w >> >> could not read overlay data from >> /home/gonzalorojas/Desktop/rendering_broca_wernicke_paper/diestroBL_cov/zstat3_lh.w" >> >> >> Why ?... How can I solve the problem ?... >> >> Sincerely, >> >> >> Gonzalo ROjas Costa >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Graphics Segfaults
by Michael Waskom 19 Nov '10

19 Nov '10

Hey Nick/Krish, Is there a way to exit tksurfer/tkmedit from a tcl script that doesn't trigger a segfault? Thanks! Cheers, Mike

1 0

Qdec errors: Mapping Label to Subjects
by Jessie Chen 18 Nov '10

18 Nov '10

Hi Everyone, I am trying to extract volume and thickness data from a list of subjects for several ROIs that Freesurfer does not automatically define (ie. Broca's area). My plan was to load a .dat table into Qdec with a column of subject IDs and a column with a dummy continuous variable. Then I would use Qdec to draw some labels, which I would later use with mris_anatomical_stats. So far, I used Qdec to draw a label and am now trying to map the label to all the subjects. However Qdec keeps giving me errors. (I'm using Freesurfer v4.0.2). (1) The first error continuously pops up, but I seem to be able to ignore it: ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 221 vtkKWQdecApp (0xdf9640): Script: FsgdfPlot_IsWindowShowing 0 Returned Error on line 1: invalid command name "FsgdfPlot_IsWindowShowing" Stack trace: invalid command name "FsgdfPlot_IsWindowShowing" while executing "FsgdfPlot_IsWindowShowing 0" I saw that a previous user also had this problem and was told that it was due to Freesurfer v4.0.2 missing the fsgdfPlot.tcl file. However, I checked my $FREESURFER_HOME/lib/tcl directory, and it appears to already have this file, so I'm not sure if this is the problem. (2) The other error I get, which seems to be causing the mri_label2label command to fail is this: ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. Label point 33: vno = 175287, max = 163842 command failed: mri_label2label --srclabel /ifs/edevel/UCLA_FREESURFER/OUTPUT/qdec/Jessie/ROI_labels/lh.insula_dummydat_11-18-10.label --srcsubject fsaverage --trgsubject 20171 --trglabel /ifs/edevel/UCLA_FREESURFER/OUTPUT/qdec/Jessie/ROI_labels/lh.insula_dummydat_11-18-10.label --regmethod surface --hemi lh This seems to be the more pressing problem, and I'm lost as to how to fix it. Any suggestions would be greatly appreciated. Thanks in advance! - Jessie Chen

2 1

Errors for talairach transformation
by liang wang 18 Nov '10

18 Nov '10

Hi FSusers, The terminal displays errors when I run "recon-all -autorecon1 -subjid ..." to get a skull-stripped brain image. The processing exits with the following errors regarding talairach transformation. Here is the talairach.xfm: MNI Transform File % tkregister2 Transform_Type = Linear; Linear_Transform = 39.07553864 15.93667889 -36.86604309 -1474.05761719 1861.34423828 844.27008057 -1897.87268066 -75416.71093750 -606.90667725 -274.30368042 622.14581299 24711.26757812 ; Any suggestions would be appreciated. Best, Liang #-------------------------------------------------------------------- #@# Talairach Failure Detection Wed Nov 17 10:15:36 EST 2010 /mnt/cd/kastner/liang/resting_state/ph_062210/fs_skull/ph/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux node37.cluster 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ph exited with ERRORS at Wed Nov 17 10:15:36 EST 2010 -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540

2 5

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer