Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

using freesurfer register program to register afni data
by Garrett McGrath 15 Feb '08

15 Feb '08

To the freesurfer people: I would like to know if there is a way to generate a new volume file from the original volume file using the matrix of transformations generated by tkregister. I need to be able to transport those changes over to afni which lacks the nice interface freesurfer has for registration. Is there currently a way to do this? or an easy way to convert those values into something usable by afni? -Garrett McGrath

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bad parcellation
by Leila BH 15 Feb '08

15 Feb '08

Hello, In some brains, the parcellation into 35 gyral based parcels is bad while the white matter seems ok, do you know how to correct this? Or what could be the raison Thanks Leila

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recon-all error messages
by Ryan Muetzel 15 Feb '08

15 Feb '08

Hello, I am getting some unusual error messages from recon-all. Both autorecon2 and autorecon3 are exiting with errors. The errors are showing up in all 10 data sets I am running. I've attached some of the log files located in '${SUBJECTS_DIR}/${SUBJID}/scripts/' for one subject. The error message I am noticing is: lnpi07.cmrr.lan 17> more recon-all.log | grep ERROR IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 15160.4 tol 0.000010 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 1999609.5 tol 0.000000 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 12913.8 tol 0.000010 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 1713191.2 tol 0.000000 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 15113.3 tol 0.000010 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 1982807.9 tol 0.000000 recon-all exited with ERRORS at Tue Feb 12 08:46:28 CST 2008 ERROR: cannot find /scratch1/nelsonm/18514/mri/lh.ribbon.mgz ERROR: loading /scratch1/nelsonm/18514/mri/lh.ribbon.mgz recon-all exited with ERRORS at Wed Feb 13 02:31:31 CST 2008 Any ideas? Thanks in advance for any help! -Ryan

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Qdec works for Leopard.
by zheng.hui＠singhealth.com.sg 14 Feb '08

14 Feb '08

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optseq2 and unique events
by Jasony Brozinsky 14 Feb '08

14 Feb '08

Hi, Can optseq2 converge on a solution when an event occurs only once? I'm having difficulty fitting a single nuisance event into a design. In each experimental block, I have 9 trials of interest, and one rare event who's HRF is unimportant to me, but which needs to be separate from the NULL condition. For the trials of interest, I'd like to keep the ITI at 2-10 seconds, but, if need be, I'd be happy to have an ITI of 60 seconds for the nuisance event if would allow this to work. Any ideas would be greatly appreciate-- the following code fails to settle on a solution: ../../optseq2 --ntp 100 --tr 2 --cost eff --tprescan 0 --psdwin 0 18 1 --ev EV1 6 3 --ev EV2 7 3 --ev EV3 8 3 --ev Nuis 11 1 --tnullmin 0 --tnullmax 12 --nsearch 1000 --focb 1000 --nkeep 100 --o output --log log --polyfit 2 P.S. The mail list's search function doesn't work for me, so please forgive me if this has been covered in a previous thread! ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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optseq2
by Julia Bender 14 Feb '08

14 Feb '08

Hi, I have a question concerning optseq2. I found that increasing the dPSD Parameter from 1/2 TR (0.92s) to 1 TR (1.84s) INCREASED the efficiency of the best schedules from about .075 to .093. I would have assumed that a more finely spaced schedule would result in better efficiency scores. Did I do (or understand) something wrong? My optseq2 command line goes as follows: /.../.../optseq2 \ --ntp 121 \ --tr 1.84 \ --tprescan 0 \ --psdwin 0 11.04 0.92 \ ## or 0 11.04 1.84 --ev trial 5.52 20 \ --ev catch 5.52 20 \ --nsearch 100 \ --nkeep 10 \ --o test \ Thank you for your support, Julia Julia Bender Humboldt Universität zu Berlin Mathematisch - Naturwissenschaftliche Fakultät II Institut für Psychologie, Abt. Klinische Psychologie Unter den Linden 6 D-10099 Berlin

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mri_convert: problem with multiple echoes in Genesis images
by Dominik Meier 13 Feb '08

13 Feb '08

Problem: mri_convert creates a NIFTI image that splits the dual echo, but pads with empty slices to the full size, e.g. a dual echo of size 256 x 256 with 108 slices will become a 4D volume with 256 x 256 x 108 x 2 instead of 256 x 256 x 54 x 2. The -nth 0 or -nth 1 option will return a volume of 54 slices, but only half of them with image data and again the lower half empty. This does not seem to happen for DICOM. Does the program look at the "echo number" tag or just de-interleave based on slice order? I noticed DICOM headers have the echo number set correctly, but Genesis headers all seem to list all slices as echo #2. If that's the source of the problem the behavior of mri_convert is not wrong (since it is getting wrong input), but unexpected. In that case: Is there an option to suppress/ignore all echo fields and read all as one volume? Environment: FREESURFER_HOME: /Programs/install/freesurfer Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1 Kernel info: Darwin 8.11.0 Power Macintosh Command: mri_convert -ot nii GE_DualEcho_PD_axial_3mm/I.001 aTestGEDual.nii Output generated $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from GE_DualEcho_PD_axial_3mm/I.001... fname_format : GE_DualEcho_PD_axial_3mm/I.%03d multi-echo genesis file detected (2 echoes)... TR=3000.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to aTestGEDual.nii... Many thanks. Dominik ______________________________________________ DOMINIK MEIER, PH.D. Center for Neurological Imaging Brigham & Women's Hospital, Harvard Medical School 221 Longwood Avenue, RF396, Boston, MA 02115 Phone: 617 278-0800 Fax: 617 264-5154

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About the average subject
by jorge luis 13 Feb '08

13 Feb '08

Hello all Hello all We are planning to perform a cross-sectional study involving two population of subjects. I think we have to choice one among two possibilities : 1-Make a single average subject for both populations and resample all the subject to this average for the statistical analysis. 2-Make two average subjects, one for each population. In the last case we are not sure what is the right posterior processing in order to get the most accurate results from the final statistical parametric map. Any help is welcome In advance thank you Jorge Phd Student ______________________________________________ ¿Con Mascota por primera vez? Sé un mejor Amigo. Entra en Yahoo! Respuestas http://es.answers.yahoo.com/info/welcome

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Binary Masks
by Anil Roy 12 Feb '08

12 Feb '08

Hello All, I want to create a binary mask volume for stg and tried the following command # mri_label2vol --label trial_labels/rh.superiortemporal.label --temp /mnt/win/MRI_data/Trial_Runs/Freesurfer/1195/mri/brainmask.mgz --o testmask.mgz The label was created using mri_annotation2label When I opened up this label in tkmedit, I could see that the cortical regions of STG are in white and everything else is in black. My questions is if it is possible to fill in the regions within this label: in other words if I can also have the white matter that the label encompasses included in the mask. Also, is there a different method that is normally used for creating binary masks? Thanks, Anil.

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[Fwd: Re: [Freesurfer] Cortical and White Matter Parcellation and Segmentation Outputs]
by lbotelho＠nmr.mgh.harvard.edu 12 Feb '08

12 Feb '08

Subject: Re: [Freesurfer] Cortical and White Matter Parcellation and Segmentation Outputs From: lbotelho(a)nmr.mgh.harvard.edu Date: Tue, February 12, 2008 4:09 pm To: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> -------------------------------------------------------------------------- Hi, 1. Some samples with the cortex/gray matter gaps in the parcellation results. Is the mri_convert --fill_parcellation utility useful here? 2. My interest and use is focused on aseg+aparc and wmparc too, thanks for pointing this clearly. 3. The sample in attachment is less than optimal (though a 3T MPRAGE, 1mm3) but to illustrate the challenge in this kind of data. Thanks for the suggestion of control points. Can you point me some reference about its usage? Best, Luis > Hi Luis, > > 1. I'll leave this for Doug. > 2. The aseg.mgz is indendent of (and produced before) the mri_segment > step (which produces the wm.mgz). In general we don't use the cortical > part > of the aseg as the surfaces in our experience are more accurate. > 3. Can you give an example of this? I would think control points could > help. Note that we don't use image intensity, but rather local gradient > maximum to position the pial surface, which should be independent of local > bias. > > cheers, > Bruce > > > On Mon, 11 Feb 2008 > lbotelho(a)nmr.mgh.harvard.edu wrote: > >> Dear FS experts, >> >> 1. There are some frequent mismatches between the white matter and >> cortex >> parcellations (aparc+aseg.mgz and wmparc.mgz) with zeroed voxels between >> them. >> >> Would suppressing the option --ribbon when running aparc2aseg either >> during cortex or white matter parcellation (or both) result in a more >> close match between aparc+aseg.mgz and wmparc.mgz? Other suggestions? >> >> >> 2. Cortex segmentation output in aseg.mgz is not uncommonly thinner than >> it should be in my data. Tweaking around the default mri_segment >> settings >> for white matter lo/hi and gray matter hi may improve it. I am still >> looking for optimal settings and the pial surface is not under control. >> Any specific suggestions? >> >> 3. These days acquiring with multichannel headcoils has become almost >> the >> norm. Even normalized data seems to suffer somehow. Particularly, >> superficial and brighter cortex is prone to produce thinner cortex >> thickness results than cortex in basal regions with less signal. Any >> workarounds? >> >> >> Many thanks, >> Luis >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > >

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