Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30091 discussions

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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unpredictable
by Joongnam Yang 05 Jan '05

05 Jan '05

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.

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CC and pons
by Joongnam Yang 04 Jan '05

04 Jan '05

Hi all, recon-all -stage1 gives me an error on "could not find corpus callosum". So, I used Tkmedit to find xyz talairach coordinates of the two structures and ran stage1 again, many times with different coordinates. "surfaces" are twisted and "filled" volume didn't look like a brain. How can I find correct coordinates? The way I did: I loaded T1 volume and aux volume and picked the approximate center of each structure. Any wise words? Thanks. Nam.

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tkmedit problem
by Kapdoskar, Shweta (NIH/CC/DRD) 04 Jan '05

04 Jan '05

Hello, I am using freesurfer on suse 9.0. I have run into problem while using tkmedit tool. When I click on the volume button in csurf , it initially turns purple and then again becomes white without doing anything. It does not spit out error messege either. Using the log messege generated , tran the following line from shell: /usr/local/freesurfer/bin/Linux/tkmedit CAM T1 -csurf (where CAM is the subject directory) .Even now it does not do anything. Plz help Shweta Kapdoskar Diagnostic Radiology Clinical Center , Rm : 1C 534 National Institutues Of Health , 9000 Rockville Pike, Bethesda , MD- 20892 Ph: 301-402-2896 Fax: 301-496-9933

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Freesurfer on Latitude X300?
by Kristine Beate Walhovd 03 Jan '05

03 Jan '05

Hi We've had some trouble with displaying the Freesurfer graphics correctly on some new stationary Dell PCs recently. I now need a new laptop, and I'm considering buying a Dell Latitude X300. I won't use it as an analysis machine, mostly just for travel, but I need to be able to display images and work with Freesurfer on it. Most features on this light-weight model are integrated so that they can't be changed, including the graphics card (855GM integrated graphics shipset - up to 64MB), so I was wondering if any of you have any expericence with running Freesurfer on this model, and if so, does it work OK? I'd be grateful for any comments. Thanks, Kristine

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