Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

Applying mask with mdi_mask
by Arash Jalalian 15 Jan '14

15 Jan '14

Hi, I would like to apply white matter mask (wm.mgz) produced by freesurfer recon-all command on FLAIR. The FLAIR and wm.mgz have different dimensions such that Flair is 512by512 while wm.mgz has 256by256 in dimensions. I tried to fix this by resizing the flair in matlab but after applying the mask the result is not good. I don't get the difference in dimension anymore though. Is there any way that I can resize a mgz volume in freesurfer? Many thanks, Arash

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Saving bbregister result as a volume
by Arash Jalalian 15 Jan '14

15 Jan '14

Hi free surfer community, I am trying to register Flair with T1 using bbregister and save the result as a volume so I can open it in my application that I am developing. I managed to obtain the register.dat and also to see the result using tkregister2. I was wondering if I can apply the transform provided in register.dat on a volume and save the output as mgz file. Thanks, Arash

2 1

mri_vol2surf - best way to avoid partial voluming?
by Josef Ling 15 Jan '14

15 Jan '14

I'd like to project functional data onto the surface for group analysis. I'd like to limit partial voluming when selecting values with mri_vol2surf. I noticed that the default projfrac = 0 for mri_vol2surf which seems to me it would select a number of values contaminated by WM. Why is the default = 0? >From the examples below, which is the soundest method of selecting representative GM only values? Please correct any errors in my understanding. :) mri_vol2surf --projfrac 0.5 --interp nearest --surf white This would select a single value closest to halfway up the normal vector from the WM vertex. mri_vol2surf --projfrac 0.5 --interp trilin --surf white This would interpolate from multiple nearby values halfway up the normal vector from the WM vertex. mri_vol2surf --projfrac-avg 0.25 0.75 0.25 --surf white Average from two values a quarter of the way up and down? Thanks

2 1

(no subject)
by Hugh Pemberton 15 Jan '14

15 Jan '14

hi guys i'm getting a 'Couldn't create output file .xdebug_tkmedit' before loading volumes, any suggestions on what I can do would be most welcome. Also got: ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : When taking a volume snapshot and then freesurfer shut down but there's no file for me to send you, I've just installed on a mac lion v5.3.0 Cheers! Hugh

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dt_recon b-values and b-vectors
by Swartz, Max 14 Jan '14

14 Jan '14

Howdy, I'm trying to run *dt_recon* on some DTI data but seem to be having some trouble with the number of b-values and b-vectors not matching the number of data frames we have (see dt_recon logfile below). Some basic parameters of our sequence are as follows: - TR = 10 s - TE = 96.2 ms - slice thickness = 4 mm - FOV = 25.6 cm 9 25.6 cm - flip angle = 90 - slice orientation= axial - matrix size = 64 x 64 - maximum b value = 1,000.65 The scan was developed from the protocol described in the following paper: http://link.springer.com/content/pdf/10.1007%2Fs00429-013-0506-x.pdf The scan is supposed to be in 30 directions, but we have 36 b-values and b-vectors. Our DTI EPI BRIK file contains 28 data frames. It is my understanding that these three values should match, but I am lost when it comes to execution of this task. Our b-values, b-vectors, and dt_recon.log file are shown below: *bval:* 0 999.4792194 999.2313486 1000.074909 998.9414996 999.2023637 1000.18885 0 999.3712757 998.6526501 999.0604376 998.6166688 1000.30379 998.9614892 0 998.9295058 998.802572 999.6841127 999.3692767 1000.26581 998.9774808 0 999.8200418 1000.64961 1000.268808 999.6821137 999.595159 999.5162001 0 999.8890059 999.7680689 999.378272 999.6581262 999.645133 998.8895267 0 *bvec:* 0 0 0 1 0 0 0.166 0.986 0 -0.11 0.664 0.74 0.901 -0.419 -0.11 -0.169 -0.601 0.781 -0.815 -0.386 0.433 0 0 0 0.656 0.366 0.66 0.582 0.8 0.143 0.9 0.259 0.35 0.693 -0.698 0.178 0.357 -0.924 -0.14 0.543 -0.488 -0.683 0 0 0 -0.525 -0.396 0.753 -0.639 0.689 0.341 -0.33 -0.013 -0.944 -0.524 -0.783 0.335 0.609 -0.065 -0.791 0.22 -0.233 -0.947 0 0 0 -0.004 -0.91 -0.415 -0.511 0.627 -0.589 0.414 0.737 0.535 -0.679 0.139 -0.721 0.884 -0.296 0.362 0.262 0.432 0.863 0 0 0 0.088 0.185 -0.979 0.294 -0.907 0.302 0.887 -0.089 -0.453 0.257 -0.443 0.859 0.086 0.867 -0.491 0.863 0.504 -0.025 0 0 0 dt_recon logfile Tue Jan 14 11:03:29 EST 2014 VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files /usr/local/freesurfer/bin/dt_recon --i /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK --s 802_ucni_FS --o /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --b /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec xoth2 swartzms /usr/share/fsl/5.0/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Tue Jan 14 11:03:29 EST 2014 cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files mri_convert /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii mri_convert /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii warning: string DATASET_NAME does not end with "~" $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK... AFNI Header Information ============================================ DATASET_RANK : spatial dims 3, sub-bricks 28 DATASET_DIMENSIONS: (64, 64, 35) TYPESTRING : 3DIM_HEAD_ANAT SCENE_DATA : view type 0, func type 2, verify 0 ORIGIN : (126.000000, -126.000000, -68.000000) DELTA : (-4.000000, 4.000000, 4.000000) IDCODE_STRING : CIR_2tEY1lHce4a BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.000000 max 128.024994 BRICK_STATS : min 0.000000 max 21.291500 BRICK_STATS : min 0.000000 max 29.162399 BRICK_STATS : min 0.000000 max 20.906200 BRICK_STATS : min 0.000000 max 20.719999 BRICK_STATS : min 0.000000 max 22.354900 BRICK_STATS : min 0.000000 max 21.723499 BRICK_STATS : min 0.000000 max 126.376999 BRICK_STATS : min 0.000000 max 21.332399 BRICK_STATS : min 0.000000 max 23.682100 BRICK_STATS : min 0.000000 max 20.807301 BRICK_STATS : min 0.000000 max 23.097000 BRICK_STATS : min 0.000000 max 23.482201 BRICK_STATS : min 0.000000 max 23.115200 BRICK_STATS : min 0.000000 max 119.787003 BRICK_STATS : min 0.000000 max 23.863899 BRICK_STATS : min 0.000000 max 22.267799 BRICK_STATS : min 0.000000 max 21.466900 BRICK_STATS : min 0.000000 max 22.947701 BRICK_STATS : min 0.000000 max 20.433399 BRICK_STATS : min 0.000000 max 20.641600 BRICK_STATS : min 0.000000 max 127.492996 BRICK_STATS : min 0.000000 max 22.346399 BRICK_STATS : min 0.000000 max 20.726400 BRICK_STATS : min 0.000000 max 21.634701 BRICK_STATS : min 0.000000 max 19.920799 BRICK_STATS : min 0.000000 max 20.998699 BRICK_STATS : min 0.000000 max 21.381701 BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 ==================================================================== INFO: number of frames dataset_rank[1] = 28 : numtypes = 28 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 128.024994 <--> actual max = 128.024704 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.291500 <--> actual max = 21.291540 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 29.162399 <--> actual max = 29.162401 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.906200 <--> actual max = 20.906200 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.719999 <--> actual max = 20.720045 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.354900 <--> actual max = 22.354910 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.723499 <--> actual max = 21.723537 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 126.376999 <--> actual max = 126.377357 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.332399 <--> actual max = 21.332430 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.682100 <--> actual max = 23.682091 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.807301 <--> actual max = 20.807331 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.097000 <--> actual max = 23.096958 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.482201 <--> actual max = 23.482182 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.115200 <--> actual max = 23.115194 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 119.787003 <--> actual max = 119.786865 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.863899 <--> actual max = 23.863934 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.267799 <--> actual max = 22.267784 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.466900 <--> actual max = 21.466867 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.947701 <--> actual max = 22.947695 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.433399 <--> actual max = 20.433388 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.641600 <--> actual max = 20.641575 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 127.492996 <--> actual max = 127.493370 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.346399 <--> actual max = 22.346439 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.726400 <--> actual max = 20.726437 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.634701 <--> actual max = 21.634733 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 19.920799 <--> actual max = 19.920761 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.998699 <--> actual max = 20.998676 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.381701 <--> actual max = 21.381670 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii... #@#------------------------------- Eddy/Motion Correct Tue Jan 14 11:03:30 EST 2014 cd /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/ectmp eddy_correct /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii 0 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0000 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0001 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0002 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0003 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0004 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0005 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0006 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0007 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0008 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0009 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0010 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0011 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0012 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0013 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0014 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0015 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0016 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0017 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0018 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0019 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0020 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0021 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0022 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0023 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0024 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0025 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0026 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0027 #@#------------------------------- Fitting Tensors Tue Jan 14 11:10:32 EST 2014 cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files mri_glmfit --y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii --glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --dti /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files cmdline mri_glmfit --y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii --glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --dti /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec sysname Linux hostname xoth2 machine x86_64 user swartzms FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii logyflag 1 usedti 1 glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files Loading y from /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii Using DTI Loading BValues from /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval Found 36 bvalues Loading BVectors from /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec Found 36 bvectorss Detected BVec file as MGH formatted Saving design matrix to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/Xg.dat Normalized matrix condition is 23.5551 Matrix condition is 1.66263e+06 Pruning voxels by thr: 50.000000 Found 255 voxels in mask Saving mask to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/mask.nii search space = 16320.000000 ERROR: dimension mismatch between y and X. y has 28 inputs, X has 36 rows. Any suggestions or insight you can provide is much appreciated. Thanks in advance, - Max -- Max Swartz Biochemistry and Biological Physics Miami University | Oxford, OH 513.886.6574

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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

2 1

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

2 3

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

2 1

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.

3 3

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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