Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

RE: [Freesurfer] Problem converting IMA files
by Kristine Beate Walhovd 20 Apr '05

20 Apr '05

Hi Doug Here it is: [brain@hippocampus ~/freesurfer]$ cd ../../../var/lab-data/barn [brain@hippocampus barn]$ cd 005 [brain@hippocampus 005]$ mri_convert -ot cor 005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA ../fp005/mri/orig/001 mri_convert -ot cor 005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA ../fp005/mri/orig/001 reading from 005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA... ERROR: could not parse /var/lab-data/barn/005/005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA ERROR: siemensRead(): /var/lab-data/barn/005/005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA When I do -it siemens instead of -ot cor it does the same thing. Thanks, Kristine -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 4/19/2005 2:42 AM To: Kristine Beate Walhovd Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem converting IMA files What was your exact command-line? Did you try adding "-it siemens"? Also, I could not read the attachment. Is it in text/ascii format? doug Kristine Beate Walhovd wrote: > > Hi > > I've tried converting IMA files (taken directly from the Siemens scanner) in Freesurfer with the command > > mri_convert -ot cor <one filename in the sequence> <output file> > > but it doesn't work. Gives an error message "cannot parse..." (see attached error message). > > I'd be grateful for any suggestions. > > Thanks, > > Kristine > > ------------------------------------------------------------------------ > Name: IMA_error.sxw > IMA_error.sxw Type: unspecified type (application/octet-stream) > Encoding: base64 > Description: IMA_error.sxw > > ------------------------------------------------------------------------ > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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License problems
by Fornito, Alexander 19 Apr '05

19 Apr '05

Hi all, We've just installed Freesurfer and tried to use mri_convert and encountered some problems. In the csurf GUI, I tried to convert a subject's image, which we keep in analyze (.img, .hdr) format, and I got the message: "Convert (subj186) failed - working on: orig/001/subj186.img" I then loaded the flat files (I.001, I.002 ... etc.) into the directory and tried to convert these. The program hangs indefinitely once I press the convert button. Next I tried to run it thought the command line on the flat files and got a message saying "No valid license key!". To the best of our knowledge, all the license files are where they should be. Any ideas on what's happening? Thanks, Alex

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Problem converting IMA files
by Kristine Beate Walhovd 19 Apr '05

19 Apr '05

Hi I've tried converting IMA files (taken directly from the Siemens scanner) in Freesurfer with the command mri_convert -ot cor <one filename in the sequence> <output file> but it doesn't work. Gives an error message "cannot parse..." (see attached error message). I'd be grateful for any suggestions. Thanks, Kristine

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Requirements for thickness analysis
by Fornito, Alexander 18 Apr '05

18 Apr '05

Hi, I am looking at running some thickness analyses on some MRI data we have already collected. I noticed that the manual states that "a minimum of two anatomical acquisitions is required for morphometric studies". Is it possible to run a valid thickness analysis in Freesurfer if I only have 1 T1 scan per person? Alternatively, a subset of our cohort have a T1 and T2, T1 and PD, or all three. Would it be possible to use a T1 and T2 instead of two T1s? Thanks for your help, Alex

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mri_convert orientation
by Wan Park 15 Apr '05

15 Apr '05

Unfortunately I only have img/hdr files. when I put mri_info I have this message: [ash:14725/mri/orig] wpark% ls 14725.hdr 14725.img [ash:14725/mri/orig] wpark% mri_info 14725.img INFO: analyzeRead(): found 1 files for /usr/local/freesurfer_package/freesurfer subjects/14725/mri/orig/14725.img ----------------------------------------------------------------- INFO: could not find /usr/local/freesurfer_package/freesurfer/subjects/14725/mr /orig/14725.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default) INFO: if not valid, please provide the information in /usr/local/freesurfer_pac age/freesurfer/subjects/14725/mri/orig/14725.mat file ----------------------------------------------------------------- Volume information for 14725.img type: analyze3d dimensions: 256 x 256 x 124 voxel sizes: 0.7812, 0.7812, 1.5000 type: SHORT (4) fov: 0.000 xstart: 0.0, xend: 0.0 ystart: 0.0, yend: 0.0 zstart: 0.0, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degre s nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.000 voxel to ras transform: -0.7812 0.0000 0.0000 100.0000 0.0000 0.7812 0.0000 -100.0000 0.0000 0.0000 1.5000 -93.0000 0.0000 0.0000 0.0000 1.0000 [ash:14725/mri/orig] wpark% I know that doing mri_convert -iid x_r x_a x_s -ijd y_r y_a y_s -ikd z_r z_a z_s I can change the orientation. In this case it would be mri_convert -iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 14725.img . My questions: 1) Are these the "default" values that the mri_convert use if I do not specify anything? (mri_convert 14725.img .) 2) If I want to change, the possible values are -1 0 and 1? Thank you very much. Wan

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threshold graph value
by Nguyen, Thang Q 14 Apr '05

14 Apr '05

Hello all, After running a mris_glm analysis, I load the sigt.w file as a overlay. When configuring the threshold value for this overlay, one can adjust the min/mid/max values on the x-axis based on the y-axis values. What do the min/mid/max values and count values on the graph indicate? Thank you, Thang Nguyen

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Vncviewer
by Jonathan Wisco 13 Apr '05

13 Apr '05

Hi Kevin, I'm not able to use vncviewer in this environment. I get the message: VNC server supports protocol version 3.3 (viewer 3.3) VNC authentication succeeded vncviewer: VNC server closed connection Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

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parcellation
by Wan Park 13 Apr '05

13 Apr '05

Hello, after parcellating some brains, I have noticed that the program "get confused" and label the occipital as frontal and viceversa. I started with img/hdr images. I suspect that this occurs because of a "wrong" direction of the original image before doing mri_convert. Is it true? How can I solve this? Thanks, Wan

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TR Units
by Doug Greve 12 Apr '05

12 Apr '05

Hi All, I just wanted to let you know about a change to the units that the TR is reported in for SOME data when converting from Siemens DICOM to analyze or bshort using unpacksdcmdir or mri_convert. I expect that this will have no effect on anyone, but I think it's a good idea to let people know, just in case. First, this does not effect functional data, which is generally the only time software would automatically read and use the TR. For analyze and bshort functional data, the TR has been and will be stored in seconds. There will be a change for non-functional data -- specifically, data whose images are not stored as mosaics in the Siemens DICOM file, but only when this data are stored in analyze or bshort formats. For these data the TR value was stored in milliseconds. It will now be stored in seconds (again only in analyze and bshort). This will have no effect on FreeSurfer reconstructions. For those in the NMR Center, this change has already been incorporated into the NMR standard and development environments. Those who run FreeSurfer and unpacking externally will be affected by the next release. Like I said, I don't think this will affect anyone, but if you think it affects you or need clarification, please let me know. thanks Doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Re: [Freesurfer] fsfast tkmedit-sess problem
by Mike Angstadt 12 Apr '05

12 Apr '05

Yeah... I figured there might be minor differences... however, I've attached tutorial.jpg which is a picture from the fs-fast documentation that is says is the output of the command: sliceview-sess -contrast omnibus -analysis sem_assoc -sf sessid -df sesspar -map fsig -slice mos -nohdr and also myresult.jpg which is what I get from the same command, after having followed all the commands in the tutorial in sequence. The other results like motion correction parameters/automatic registration/etc come up with similar numbers to theirs, though not exact which makes sense if the binaries have changed. However these two pictures appear very different. -Mike At 12:39 PM 4/12/2005 -0400, Brian T. Quinn wrote: >hi Mike- > >in response to your 2nd question, the manual was created a few years ago >and the binaries have changed since then, so the images won't look exactly >the same, but should not be drastically different. > >thanks, >brian t. quinn > >On Tue, 12 Apr 2005, Mike Angstadt wrote: > >>Hi, >> I've just started to look at fs-fast for analyzing data and was >> following along with the tutorial data using the fs-fast documentation >> from the website. My problem arises when I try to view the data with tkmedit: >>>tkmedit-sess -sf sessid -df sesspar -a sem_assoc -c omnibus -map fsig >>-------------------------------------------------------------- >>tkmedit-sess logfile is /data/freesurfer/scratch/bert/log/tkmedit-sess.log >>-------------------------------------------------------------- >>INFO: Found session in: /data/freesurfer/Sessions//bert-functional >>INFO: Found session in: /data/freesurfer/Sessions//bert-functional >>ERROR: cannot find >>/data/freesurfer/scratch/bert//data/freesurfer/Sessions//bert-functional/bold/register.dat >> >>I don't understand why it's adding the current directory to the beginning >>of the path where it should be looking for the register.dat file. The >>path should just be >>/data/freesurfer/Sessions//bert-functional/bold/register.dat, where the >>registration file is located. >> >>Any thoughts? >> >>Also, as a side note... has the tutorial data been updated since the >>documentation was made? Because following alone with exactly the >>commands given in the documentation does not yield the same visual >>results for me as the example images. >> >>-Mike >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >brian t. quinn

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