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30133 discussions

Hippocampal Subfield Segmentation
by Germeyan, Sierra (NIH/NINDS) [F] 14 Jan '14

14 Jan '14

Hi everyone, In using Van Leemput's -hippo-subfields flag as part of the recon-all script to obtain hippocampal subfield volumes, my lab has determined that larger subfields are more relevant for our purposes clinically/surgically. Is there a way to group the fimbria/CA1/2,3/4,DG/presubiculum/subiculum/hippocampal fissure/etc. subfields such that they correspond to the head, body, and tail of the hippocampus? I am aware that the subfield "hippocampus" refers to part of the tail of the hippocampus, but beyond that, it is unclear how these subfields should be categorized. Thanks for the help! Sierra Germeyan, B.A. Clinical Epilepsy Section, NINDS, NIH

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inter-hemispheric comparison
by Shani Ben Amitay 14 Jan '14

14 Jan '14

Hello freesurfers I would like to preform inter-hemispheric comparison (or hemispheric asymmetry) for a volume of a single subject. what would be the best way to do it? Thanks Shani

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hippo-subfield
by stdp82＠virgilio.it 14 Jan '14

14 Jan '14

Hi list, I have some question regarding hippo-subfield parcellation.If I understand the final results are thickness of each ROI but assuming a voxel of 0.5x0.5x0.5.Therefore, a correction is request. A-How is the best way to do it?B-Correction for mean thickness or ICV is advised? C-Is possible use qdec GUI or other GUI to performe a vertex by vertex comparison?D-Is there a way to visualize the groups differences in a map? Thanks and best regards, Stefano

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Re: [Freesurfer] brain orientation in qdecDouglas N Greve
by Douglas Greve 13 Jan '14

13 Jan '14

Sounds like it is some problem with the display libraries. I think someone else was having the same problem recently (ie, hemisphere displayed upside down in tksurfer). Does anyone remember? Zeke? doug On 1/12/14 5:03 AM, Schweren, LJS (med) wrote: > No, in Freeview I encountered no such problems. Also in tkmedit the brains appear in normal orientation. > Also, the scale bars and titles are displayed upside down in tksurfer. > > Best, Lizanne > > > > Does the same thing happen in freeview? > On 01/06/2014 04:45 AM, L. Schweren wrote: > > > > Dear experts, > > > > I ran recon-all with qcache. When loading the right hemisphere of > > fsaverage (or any other surface reconstruction) into tksurfer (for > > example command: tksurfer fsaverage rh white), the left hemisphere > > surface is displayed, and it is upside down. When I import annotations > > they load in the same orientation as the surface. However, the > > coordinates and the labels, displayed in the Tksurfer Tools window, > > are not. For example, when I move the cursor to the temporal lobe, the > > label says it’s postcentral. I do not mind manually turning the > > surfaces in tksurfer, but I do need to be sure I am looking at the > > correct hemispheres, coordinates and labels. > > > > I hope you can help me solve this. Thank you in advance. > > > > Best wishes, > > > > Lizanne > > > > > > > > _______________________________________________ > > 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 > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > ------------------------------------------------------------------------ > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de > geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik > maken van dit bericht, het niet openbaar maken of op enige wijze > verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk > gesteld worden voor een incomplete aankomst of vertraging van dit > verzonden bericht. > > The contents of this message are confidential and only intended for > the eyes of the addressee(s). Others than the addressee(s) are not > allowed to use this message, to make it public or to distribute or > multiply this message in any way. The UMCG cannot be held responsible > for incomplete reception or delay of this transferred message.

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mri_convert fails to properly convert DTI dicoms
by Jiahe Zhang 13 Jan '14

13 Jan '14

Hi, I had a strange problem trying to convert DTI dicoms. When I used the following command to convert a raw dicom to nifti image, I obtained a 64-volume nifti that only contains one horizontal slice of the brain. mri_convert [input Dicom] [output nifti name] Does anyone have ideas for why this might happen? Thanks. Best, Jiahe Here is the full log if it helps. [cobham:dti] (nmr-stable53-env) mri_convert /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom/MR.1.3.12.2.1107.5.2.32.35006.2013043010182341278836940 dti_test.nii mri_convert /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom/MR.1.3.12.2.1107.5.2.32.35006.2013043010182341278836940 dti_test.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom/MR.1.3.12.2.1107.5.2.32.35006.2013043010182341278836940... Getting Series No Scanning Directory INFO: Found 3971 files in /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom INFO: Scanning for Series Number 53 INFO: found 64 files in series INFO: loading series header info. INFO: sorting. RunNo = 52 INFO: (128 128 1), nframes = 64, ismosaic=0 PE Dir unknown UNKNOWN AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 0.043 0.047 -0.105; -0.045 0.998 0.053 -6.588; -0.045 -0.055 0.998 -24.537; 0.000 0.000 0.000 1.000; This looks like an MGH DTI volume DTI is in non-moasic form, so cannot extract bvals/bvects FileName /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom/MR.1.3.12.2.1107.5.2.32.35006.2013043010182341278836940 Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName NMASA_035_130430 Date and time StudyDate 20130430 StudyTime 075408.863000 SeriesTime 101828.978000 AcqTime 100900.672500 Acquisition parameters PulseSeq unknown Protocol DIFFUSION_HighRes PhEncDir unknown EchoNo 1 FlipAngle 0 EchoTime 0 InversionTime -1 RepetitionTime 0 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 52 SeriesNo 53 ImageNo 1 NImageRows 128 NImageCols 128 NFrames 64 SliceArraylSize 64 IsMosaic 0 ImgPos 0.0000 0.0000 0.0000 VolRes 0.0000 0.0000 0.0000 VolDim 128 128 1 Vc 0.0000 0.0000 0.0000 Vr 0.0000 0.0000 0.0000 Vs -0.0300 -0.6266 0.7788 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=0.00, TE=0.00, TI=-1.00, flip angle=0.00 i_ras = (0, 0, 0) j_ras = (0, 0, 0) k_ras = (-0.0299672, -0.626615, 0.778753) writing to dti_test.nii... WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... ... continuing.

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pial_lgi in QDEC
by Sophie Maingault 13 Jan '14

13 Jan '14

Dear FS experts, I followed this page to measure LGI : http://freesurfer.net/fswiki/LGI I wanted to use it in QDEC, so after running recon-all cache for pial_lgi, I created the $SUBJECTS_DIR/qdec/.Qdecrc with MEASURE1 = pial_lgi but I don't see it in the measures menu. Do you know why ? Best regards. Sophie Maingault

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Fwd: Re: problem with bvecs file with new (12/13) TRACULA code
by Salil Soman 13 Jan '14

13 Jan '14

---------- Forwarded message ---------- From: "Salil Soman" <salsoman(a)stanford.edu> Date: Jan 12, 2014 1:28 PM Subject: Re: problem with bvecs file with new (12/13) TRACULA code To: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> Cc: Hi, > > Thank you for your email. Taking the .bval and bvec files outputed by > dcm2nii (which are row format) and transposing them to column format was > resulting in the blank rows that were causing troubles. Running this > command got rid of the problems and allowed trac-all prep / bedp / and path > to complete without errors: > > sed '/^\s*$/d' > > > Thanks, > > Sal > > > On Fri, Jan 10, 2014 at 3:57 PM, Anastasia Yendiki < > ayendiki(a)nmr.mgh.harvard.edu> wrote: > >> >> Hi Sal - It looks like a problem with the spaces at the end of the lines >> of the bvecs file. If you remove those spaces, it should work. Thanks for >> bringing this to my attention - the row-formatted bvecs files are new in >> this version and I'll make sure to allow them to have spaces at the end of >> the lines in the future. >> >> a.y >> >> >> On Thu, 9 Jan 2014, Salil Soman wrote: >> >> Hi, >>> >>> I am re-running GE acquired 3T product DTI data which ran without >>> trouble through the older tracula code. >>> However, now when I run the code, the bvec file that gets generated has >>> an extra 0 placed at the very end, >>> and then trac-all -prep eventually fails because it complains the bvec >>> and bvals files have non-matching >>> number of entries. I do have the dorotbvecs option set to 1 (as I had >>> before). Any suggestions on what I am >>> doing incorrectly would be greatly appreciated. I have attached the bvec >>> and bval files I am providing a >>> input. >>> >>> Best wishes, >>> >>> Sal >>> -- >>> Salil Soman, MD, MS >>> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory >>> Fellow - Palo Alto War Related Illness and Injury Study Center >>> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care >>> System >>> >>> >>> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care > System >

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DOSS or DODS
by amirhossein manzouri 13 Jan '14

13 Jan '14

Hello all, I am using Qdec (version5.1) to study cortical thickness differences between groups having Age as nuisance covariate. I do not have assumption if the groups are different or not . Using DODS and DOSS gives me completely different results. We have three groups including 41, 39, and 24 subjects in each. My question is which results design matrix type is more reliable for such a study? And also what if I include a covariate of interest in my comparison? Thanks in advance, Best regards, Amirhossein Manzouri

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Tracula Error: bvecs and bvals don't have the same number of entries
by Francesco Baldacchini 13 Jan '14

13 Jan '14

Hi everybody, I'm trying to run the* trac all -prep *command but after some times I get this error "bvecs and bvals don't have the same number of entries". I've checked my bvals and bvecs, which are in attach, but they seems to be formatted in the right way. What can I do? Thanks, Francesco Baldacchini

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Sphere vertices
by Chris McNorgan 13 Jan '14

13 Jan '14

Hi, I wanted to confirm whether spherical inflation generates meshes with the same number of vertices across individuals? Or would you have to use something like mri_surf2surf to map everyone's sphere to a template sphere? Thanks, Chris

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