Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Re: [Freesurfer] normalization failed
by Joongnam Yang 07 Jan '05

07 Jan '05

Hi, For one subject's data, "process volume" didn't get the skull stripped. The skull was there intact in "brain" volumes. To correct it, I used "expert preferences" and used "don't use watershed analyze", which led to most of the skull removed in "brain" volumes. But still there are pieces of the skull left. (I tried "preflooding" option, no difference). Any suggestions on how to trim the leftovers of the skull? Thanks. Nam.

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Re: [Freesurfer] normalization failed
by Joongnam Yang 06 Jan '05

06 Jan '05

Thanks Bruce, How would I specify the new talairach.xfm in the run of recon-all -stage1. If I copy the new file into the usual /mri/transforms directory, it's overwritten during the recon-all process. Comments are appreciated. Nam. >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 01/06/05 4:55 PM >>> check the talairach transform On Thu, 6 Jan 2005, Joongnam Yang wrote: > Hi, > > During recon-all -stage1 running, I got the following error. > > ....... > MRInormalize: could not find any valid peaks > No such file or directory > mri_normalize: normalization failed > No such file or directory > ERROR: mri_normalize exited with non-zero status > - > Any suggestion would be appreciated. > > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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ascii information file for a label
by Sergey A Solovyev 06 Jan '05

06 Jan '05

Hi, Tksurfer provides a nice tool to display information such as vertex index, spherical coordinates (rho, theta), values of overlaid functionals as a function of the mouse/cursor position. I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? Something like >mris_convert -p *h.patch.flat *h.patch.flat.asc that in addition to vertex number, provides spherical coordinates, AND values of functional overlay(s) for a patch, or better for a label. Thank you, Serge

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normalization failed
by Joongnam Yang 06 Jan '05

06 Jan '05

Hi, During recon-all -stage1 running, I got the following error. ....... MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status - Any suggestion would be appreciated. Nam.

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mri_convert
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, After I ran mri_convert, I saw the "orig" volumes. Are the red crosses in the image significant in that the center cross should be the center of the brain in terms of left and right hemispheres? It is not in the center, much away from the center in my "orig" volumes. If it has to be corrected how would I do it? I tried mri_convert -ic option, to no avaible. Comments are appreciated. Nam.

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3dvolreg motion correction
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, The man page shows the following for the AFNI motion correction binary. 3dvolreg [options] dataset Registers each 3D sub-brick from the input dataset to the base brick. 'dataset' may contain a sub-brick selector list. Would someone tell me how to specify "dataset"? Is it *.img or COR-* or anything else? Thanks in advance. Nam.

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annotation and labels
by Rutvik Desai 05 Jan '05

05 Jan '05

I parcellated a subject using parcellate_subject, and was trying to see the labels. Doing File->Label->Import annotation and selecting lh.aparc.annot makes tksurfer crash. Trying to convert annotations to labels using mri_annotation2label givies a bus error. What could be the problem? Running Max OSX 10.3.6. thanks, Rutvik ---------- % mri_annotation2label --subject 137 --hemi lh --outdir ./label --table $FREESURFER_HOME/Simple_surface_labels2002.txt subject = 137 annotation = aparc hemi = lh outdir = (null) surface = white Reading surface /usr/local/freesurfer/subjects/137/surf/lh.white Loading annotations from /usr/local/freesurfer/subjects/137/label/lh.aparc.annot reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[22282]: arguments too large: 3221220448,520 CTABreadFrom: could not allocate -1073746848 bin table Cannot allocate memory Bus error %

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two questions
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, Sounds like trivial questions... (1) How do you check if the talairach.xfm is OK? (2) Either during the command-line option of recon-all -stage 1 thru 4, when do you use tkregister2 for registeration? Thanks for the help. Nam.

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not symmetrical
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, For another subject, the inflated surfaces for left and right are not right after "create surface" in csurf GUI. They are not symmetrically cut. The brain seems to have been cut not through the midline, but a notch toward left hemisphere. When I looked at wm or T1 surfaces, they show that they are not symmetrical, the right hemisphere taking some of the left hemisphere. When the cut is not right, what should I do? Comments appreciated. Nam.

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Re: [Freesurfer] unpredictable
by evelina＠nmr.mgh.harvard.edu 05 Jan '05

05 Jan '05

Nam, did the command-lines work for those same subjects for which the GUI failed? I prefer the command-line operation, in any case. > Hi Nam, > > this depends on the quality of the scans, the subject positioning, and > the quality of the MNI talairaching. > > Bruce > > On Wed, 5 Jan 2005, Joongnam Yang > wrote: > > > Hi, > > > > For some subjects' data, pure Csurf GUI works, while for other subjects > > Csurf GUI complains, giving errors during "create surface", upon which I > > have to run the command-line option "recon-all -stage1" with CC and pons > > coordinates. > > > > Is it ture, I mean the Csurf GUI is unpredictable, because of the nature of > > the algorithm? > > > > Comments appreciated. > > > > Nam. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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