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30063 discussions

mri_convert: dicom to nifti 4D
by Thomas, Adam (NIH/NIMH) [E] 07 Jul '06

07 Jul '06

I seem to be having some trouble converting a 4D time series from dicom to nifti format using mri_convert. Rather than outputting 144 frames of 38 slices each, it creates a volume with a single frame of 5472 slices (see below). Is there an argument I should be using to specify number of frames? I think there was a post on this back in April (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02656.htm l), but I can't seem to find an answer in the archives. Thanks, -Adam [adamt@master 004]$ mri_convert axialepi-00001.dcm test.nii mri_convert axialepi-00001.dcm test.nii reading from axialepi-00001.dcm... 5472 DICOM 3.0 files in list Found 5472 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 5472. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /misc/radium0/adamt/mirrorTracking/XX/2006-02-11-S2/XXXXXXXX/2006_02_11- 15667/004/axialepi-00001.dcm Date and time study date 20060211 study time 170403 series time 172558 acquisition time 172558 Identification patient name XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX manufacturer GE MEDICAL SYSTEMS Dimensions number of rows 64 number of columns 64 number of frames 5472 pixel width 3.28125 pixel height 3.28125 slice thickness 3.2 field of view 210 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 30 repetition time 2500 inversion time 0 echo number 1 flip angle 1.5708 bits allocated 16 Spatial information first image position -103.359 -132.14 75.59 last image position -103.359 -132.14 -42.81 image orientation 1 -0 0 -0 1 0 ------------------------------------------------- TR=2500.00, 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 test.nii... [adamt@master 004]$ --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370

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howto cut "canonical" occipital patches?
by Sebastian Moeller 07 Jul '06

07 Jul '06

Hi All, I recently finished the surface transform of my first human brain with freesurfer. (All I had to do was run recon-all autorecon1, autorecon2 and autorecon3 in sequence, no manual edits necessary, joy, and that after doing monkey surfaces that required manual intervention at all polssible steps ;). Thanks for this great tool). Now I really would like to produce flat maps of my subjects occipital pole, and there is my question. What are the "canonical" cuts needed to produce "standard" occipital pole flat maps? I guess one cut will have to be along the calcarine sulcus, but how about the temporal lobe (I really would like to keep FFA and the STS if possible...). Thanks in advance & ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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some questions about thickness map
by R. Chen 07 Jul '06

07 Jul '06

Hi, I want to know the what the thickness map represents. As Bruce said in 'measuring the thickness of human cerebral cortex from magnetic resonance images', page 1, paragraph 6, 'The distance between these two surfaces then gives the thickness of the cortical gray matter at any point.' What physical variable are measured in thickness map? Is it the distance between a vertex in gray/white surface and the corresponding vertex in pial surface. Whether each vertex in gray/white surface has a match point in pial surface, and vice verse? If true, this means there is a 1-1 mapping between those two surfaces. If thickness map represents gray matter. How can we get the average thickness of a ROI. Can we draw a ROI in pial surface, then overlay the thickness map to pial surface, and compute the average. Thanks, Ron --------------------------------- Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta.

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macosx 10.3.9 and scuba 3.0.3
by Sebastian Moeller 06 Jul '06

06 Jul '06

Hi All, just tried 3.0.3 panther, scuba still crashes and takes X11 with it. ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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scuba and macosx 10.3.9
by Sebastian Moeller 06 Jul '06

06 Jul '06

Hi All, on my trusty iBook (10.3.9) trying to run scuba (from the 3.0.1 panther version) crashes the X-server (well Xquartz the windowmanager dies, taking the whole X11 with it). Will try 3.0.3. ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Autoseg and surface extraction
by Satrajit Ghosh 05 Jul '06

05 Jul '06

Dear Bruce, Does the autoseg information get used for surface extraction? For example, when autoseg classfies the ventricles and basalganglia, are the surface extraction routines supposed to treat these voxels as part of white matter and continue? Ideally at the end of the day any place where the surface runs through a non-cortical patch, the thickness would be zero? Thanks, Satra

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STG Volume
by Ajith Kumar U 05 Jul '06

05 Jul '06

Hello all, My lab needs to obtain STG volumes for a bunch of minc files. I've been going through the wiki and found that recon-all has to be run to first convert the files into mgz after which it will automatically generate a file with the volumes. I ran it on one of our computers (P4 @ 3.8 Ghz with 4 gigs of RAM) and it took 23 hrs. I was wondering if this is the amount of time it'll always take or if there's a way to bypass everything so that I can just obtain STG volumes. Any help is appreciated. Thanks - Aju. ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. **************************************************

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mri_surfcluster command syntax
by d.g.lawyer＠medisin.uio.no 05 Jul '06

05 Jul '06

Hi, An oddity re: command syntax for mri_surfcluster. The --ocp flag writes the file sig.cluster.mgh. However, when I also include the --cwsig flag the file sig.cluster.mgh is not generated. Currently I run the command twice, once to generate the sig.cluster.mgh, and once to generate the cluster-wise_sig.mgh. I suspect there is a better way. I am using FreeSurfer 3 stable centos4 mri_surf version 1.26, 2006/02/22

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cluster analysis with mri_glmfit
by d.g.lawyer＠medisin.uio.no 05 Jul '06

05 Jul '06

Hi, I have a couple of specific questions regarding cluster analysis with mri_glmfit that weren't answered at the course the other week and on which the documentation is slightly vauge. My data includes continuous variables (age and IQ, matching the documentaion!) so I should use MC simulation instead of permutation. I have 70 subjects in each group (case/control). The course notes say I can use the mc-z if I have O(80) subjects. How can I tell if I have enough subjects; is there a statistical test that would show if the outputs are reasonable? I would think 70 is close enough to 80, but would like to be able to test it as I assume it is going to depend to a certain extent on the data. The notes say I need to supply the fwhm of the residual. This value is easy to find in the y file, but it is not clear how to specify it to mri_glmfit. Do we use the --fwhm flag as in the example on page 104/202 in the coursebook? Note that the example uses mc-full, not mc-z, and that the --fwhm flag an arguement to mri_glmfit, not a part of the --sim flag. Finally, with regard to the clustering. The commmand as given in the course notes (pg 104/202) works, but the example does not match mri_surfcluster --help. Specifically, the --help text does not mention (that I could see) the --src flag or the --ocp flag. We are using the example from the course as our template. What is the output of the --ocp flag? Thanks!

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registration problems
by bdragans＠uke.uni-hamburg.de 04 Jul '06

04 Jul '06

Dear freesurfers, I got some problems running the mri_ca_register bit of recon-all. The script suddenly brakes down while labeling for the right thalamus is running. Occured twice on the same spot... my specifications: freesurfer-Darwin-tiger-stable-pub-v3.0.3 recon.log file is attached any help is greatly appreciated many thanks

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