Freesurfer

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30076 discussions

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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Cortical and White Matter Parcellation and Segmentation Outputs
by lbotelho＠nmr.mgh.harvard.edu 11 Feb '08

11 Feb '08

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

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SPGR format
by a.m.fjell＠psykologi.uio.no 11 Feb '08

11 Feb '08

Hi, we have problems converting scans obtained from a GE scanner with a T1-weighted 3-D spoiled gradient recalled (SPGR) sequence to anything freesurfer can read. Any tips? Thanks! - Anders

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freesurfer version difference
by Mithra 11 Feb '08

11 Feb '08

Hello, We used Freesurfer version 4.0.0 for a many of our subjects and version 4.0.1 for the other subjects. Will there be a difference between both the versions. We are comparing individual subjects brain (aseg stats) at 2 different instances. It so happens we are comparing the same subject's brain done with version 4.0.0 with his later structural scan analyzed with version 4.0.1. We are looking at the Hippocampus and Amygdala volumes. Thanks. -- Regards, Mithra Imaging Research Center University of Texas, Austin 3925-B W Braker Lane Austin. TX - 78759 Tel: (512) 232-5725 Fax: (512) 232-4202 www.irc.utexas.edu

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recon-all with DICOM vs. mgz inputs - volume differences
by Jennifer C. Britton 11 Feb '08

11 Feb '08

On the freesurfer wiki, it says that recon-all can be done with DICOM inputs in addition to mgz inputs. In doing recon-all using DICOM or mgz (created via unpacksdcmdir), the volumetric values obtained using mris_volume and mris_wm_volume are different. For example in one subject, with DICOM inputs: pial 505865 and white matter volume 166713. with mgz inputs: pial 510322 and white matter volume 167030. The white matter seems to be fairly close but the pial volume is off by nearly 4000. Can someone explain why there is this difference and which value we should believe? Thanks, Jennifer

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