Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

how to register subcortical segmentation with the original image
by Shahabuddin Ansari 24 Mar '06

24 Mar '06

Hello, I have subcortical segmentations from freesurfer. I have automatically extracted one of the segmented objects (binary). I need to get the grayscale map of the object and do not know how to register the segmented object with the original image (analyze) so it can be overlayed for masking? Any comments? Thanks Shahab --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.

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load_mgh question
by camilo＠nmr.mgh.harvard.edu 24 Mar '06

24 Mar '06

Hi Freesurfer help, Thanks for the prompt response. I now am using the load_mgh function but it is giving me the following error: ??? SWITCH expression must be a scalar or string constant. Error in ==> load_mgh at 126 switch type Does anyone have an idea why this is happening? Thanks, Camilo

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Question about format conversion
by camilo＠nmr.mgh.harvard.edu 24 Mar '06

24 Mar '06

Hi Freesurfer Help, I am trying to get the wm.mgz file into matlab. Is there a way to change the mgz into dicom format, or any othe matlab compatible formats? Thanks, Camilo

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norm.mgz
by Vasanth Pappu 24 Mar '06

24 Mar '06

Hi, I am using recon-all and the norm.mgz's so far are only about half the brain. I checked the input volumes and looked though the output to std and everything seemed fine, so I am not sure what to do: on machine vader source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /autofs/space/boba_001/users/nrecon/ which mri_ca_normalize /usr/local/freesurfer/stable/bin//mri_ca_normalize cd /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz output: using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=56.0 using (109, 110, 82) as brain centroid... mean wm in atlas = 109, using box (94,96,73) --> (123, 124,90) to find MRI wm before smoothing, mri peak at 484 after smoothing, mri peak at 484, scaling input intensities by 0.225 scaling channel 0 by 0.224939 using 242283 sample points... INFO: compute sample coordinates transform 1.724 -0.639 -2.451 142.880; 0.122 1.661 -0.265 -85.128; 2.012 0.112 1.598 -322.680; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (121, 85, 50) --> (177, 152, 94) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 87 of 225 (38.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (116, 86, 62) --> (172, 156, 102) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 108.0 90 of 179 (50.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (132, 135, 50) --> (150, 158, 68) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 96.0 18 of 52 (34.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (123, 136, 61) --> (144, 161, 76) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 102.0 23 of 58 (39.7%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (138, 130, 62) --> (152, 170, 78) Brain_Stem: limiting intensities to 89.0 --> 97.0 37 of 66 (56.1%) samples deleted using 580 total control points for intensity normalization... bias field = 1.037 +- 0.088 0 of 219 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 29 seconds. But when I look at norm.mgz, the whole brain is not shown: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/norm.mgz I checked the inputs brainmask.mgz and nu.mgz, and they seem ok: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/brainmask.mgz tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/nu.mgz how do I check if the transforms/talairach.lta is ok? Thanks, Vasanth

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fsaverage
by Sasha Wolosin 24 Mar '06

24 Mar '06

Is fsaverage used in recon-all processing? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: [martinos-tech] FreeSurfer NIFTI with SPM and AFNI
by Doug Greve 23 Mar '06

23 Mar '06

I've just fixed a bug in the way FreeSurfer produces *uncompressed* NIFTI files. It actually always produced *compressed* files, even if the extetion was just .nii and not .nii.gz. I have fixed this, and it will be live in dev tomorrow and live in stable at the next update. I've successfully loaded uncompressed files into both SPM and AFNI, but failed on compressed. Does anyone know if they even can read compressed? Both compressed and uncompressed work with FSL. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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still trouble with this motioncor problem
by Daniel Goldenholz 23 Mar '06

23 Mar '06

Hi I emailed a little while ago about this, but I haven't heard any solutions yet. As a check, I re-ran recon-all again this morning on a local machine. Still crashing. Here is the output: > recon-all -s $SUBJECT -motioncor INFO: SUBJECTS_DIR is /autofs/space/megraid_043/seder/freesurfer Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev -rw-rw-r-- 1 dwakeman megclin 27336 Mar 10 18:01 /autofs/space/megraid_043/seder/freesurfer/nmr00069/scripts/recon-all.log Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30 CST 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Thu Mar 23 11:37:22 EST 2006 Found 2 runs /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz #----------------------------------------------- /autofs/space/megraid_043/seder/freesurfer/nmr00069 mri_motion_correct.fsl -o /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz -wild /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz tmpdir is /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz Thu Mar 23 11:37:32 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069 mri_convert /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img -odt float reading from /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz... TR=2000.00, TE=3.25, TI=950.00, flip angle=7.00 i_ras = (-0, -1, -5.55112e-17) j_ras = (-0.0401318, -0, -0.999194) k_ras = (-0.999194, -0, 0.0401318) changing data type from 4 to 3 (noscale = 0)... writing to /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img... Analyze Output Matrix -0.000 -0.040 -0.999 91.684; -1.000 -0.000 -0.000 129.675; -0.000 -0.999 0.040 117.569; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz Thu Mar 23 11:37:37 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069 mri_convert /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img -odt float reading from /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz... TR=2000.00, TE=3.25, TI=950.00, flip angle=7.00 i_ras = (-0, -1, -5.55112e-17) j_ras = (-0.0401318, -0, -0.999194) k_ras = (-0.999194, -0, 0.0401318) changing data type from 4 to 3 (noscale = 0)... writing to /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img... Analyze Output Matrix -0.000 -0.040 -0.999 91.684; -1.000 -0.000 -0.000 129.675; -0.000 -0.999 0.040 117.569; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img Thu Mar 23 11:37:43 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069 fsl_rigid_register -maxangle 90 -r /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img -i /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img -o /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img -tmpdir /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Thu Mar 23 11:37:43 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /autofs/space/megraid_043/seder/freesurfer/nmr00069 calling eval flirt -in /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.hdr -out /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.hdr -omat /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image Started at Thu Mar 23 11:37:43 EST 2006 Ended at Thu Mar 23 11:43:33 EST 2006 fsl_rigid_register Done To check results, run: tkmedit -f /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img -aux /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img mv /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img ----------------------------------------- Averaging Thu Mar 23 11:43:33 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069 inhibiting isotropic volume interpolation 1 of 2: reading /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img... 2 of 2: reading /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img... INFO: analyzeRead(): min = 0, max = 1543 ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 158, k=158, row = 0 nread = 0, nexpected = 256 fname = height = 256 width = 256 depth = 160 nframe = 1 imnr0 = 1 imnr1 = 160 xnum = 256 ynum = 256 fov = 256.000000 thick = 1.000000 xstart = -128.000000 xend = 128.000000 ystart = -128.000000 yend = 128.000000 zstart = -80.000000 zend = 80.000000 type = 3 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 x ras = 0.000000 -1.000000 -0.000000 y ras = -0.040132 0.000000 -0.999194 z ras = -0.999194 0.000000 0.040132 c ras = 5.572693 0.674698 -8.076317 det(xyz_ras) = -1.000000 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format = analyzeRead2(): error reading from file /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img mri_average: MRIread(/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img) failed Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30 CST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Mar 23 11:43:38 EST 2006 -- Daniel Goldenholz ----------------------------------------------------- Cell: 617-935-9421 http://people.bu.edu/danielg/ "Mavet v'chaim b'yad halashon" "Life and death are in the hands of language" - Proverbs 18:21

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Re: [Freesurfer] --conform option
by Bruce Fischl 23 Mar '06

23 Mar '06

thanks Bob, let us know if the problem is on our end and we'll fix it. Bruce On Thu, 23 Mar 2006, Cox, Robert W. (NIH/NIMH) [E] wrote: > AFNI does read the minc orientation fields. It does not read .mgh files. If there is a problem with the minc inpiut, we'll need to get a sample file for diagnosis. > RW Cox - SSCC/NIMH/NIH/DHHS/USA > > -----Original Message----- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Pellegrini, Stefano (NIH/NINDS) [F] <pellegrinis(a)ninds.nih.gov> > CC: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>; Cox, Robert W. (NIH/NIMH) [E] <robertcox(a)mail.nih.gov>; Ziad S. Saad <ziad(a)nih.gov> > Sent: Thu Mar 23 10:29:58 2006 > Subject: RE: [Freesurfer] --conform option > > Hi Stefano, > > the orientation info is stored in the header, and can be accessed with > mri_info. It should be propagated to AFNI, not sure why it's not. Bob and > Ziad: have you had any trouble with losing the direction cosines when > converting things from .mgz? > > cheers, > Bruce > > > On Thu, 23 Mar 2006, Pellegrini, Stefano (NIH/NINDS) > [F] wrote: > >> >> thanks Bruce, >> >> actually it is ok if I view it with tkmedit. But if I try to convert it >> to minc format and I try to view it with AFNI (for istance), I get the >> wrong orientation. Is there any way to automatically know which kind of >> orientation I am working with, so that I can include it in a script when >> I want to use the conversion to the minc format? thanks again, >> >> -stefano >> >> >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Thu 3/23/2006 10:19 AM >> To: Pellegrini, Stefano (NIH/NINDS) [F] >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] --conform option >> >> Hi Stefano, >> >> the --conform does several things to the input volume to put it into a >> format we expect. If you bring it up in tkmedit and it properly shows you >> the various directions (e.g. the "coronal" view is indeed coronal) then >> you should be fine. >> >> Bruce >> On Thu, 23 Mar 2006, Pellegrini, Stefano (NIH/NINDS) [F] >> wrote: >> >>> Hi everybody, >>> >>> can anybody explain to me why when I use mri_convert with the --conform option with an input volume RAS oriented (let's say it is raw_mean.mgz) I get as output a volume LIA oriented (let's say it is orig.mgz)? is that ok? >>> thanks, >>> >>> -stefano >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> >> > > >

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recon-all bug in -normalization2 ?
by skenny＠uchicago.edu 23 Mar '06

23 Mar '06

hi all, i noticed this bug in the recon-all script. according to the reconAllDevTable, if recon-all is called with just the -normalization2 flag it should call both mri_normalize and mri_mask. however, in looking at the script it seems to only call mri_normalize. so, if using that flag you should be aware that it will not call both processes and brain.finalsurfs.mgz will not be produced. this issue came up as i was working on parallelizing; but it was pointed out to me that this info would be useful to others as well, so i'm starting a new thread. the solution i used was to change the recon-all script so that it calls both processes with that flag...or you could just explicitly call mri_mask on the commandline after you've run recon-all with the -normalization2 flag. sarah

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mri_convert problems
by ingeam＠student.sv.uio.no 23 Mar '06

23 Mar '06

Hi, I'm a new Freesurfer user, currently working with Fjell and Walhovd in Oslo. When trying to convert some new scans with mri_convert there seems to be a problem with the reconstruction, also the signal intensity is in the 300-500 range. See attached image. It does not return any errors. Could someone please point me in the right direction here? Thank you Inge K Amlien Running on: Freesurfer centos4 x86_64 stable 3.0 Fedore Core4 Output from mri_convert: mri_convert /labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_002.dcm /labdata/lab-data/testinge/testE0000002/mri/orig/001.mgz reading from /labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_002.dcm... Getting Series No INFO: Found 130 files in /labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 128 files in series INFO: loading series header info. INFO: slice direction constructed from image direction cosines. INFO: sorting. RunNo = 1 INFO: Handedness changed to left-handed. INFO: (512 512 128), nframes = 1, ismosaic=0 FileName /labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_716.dcm Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Symphony PatientName E0000002 Date and time StudyDate 20051121 StudyTime 094537.984000 SeriesTime 095542.281000 AcqTime 094657.180012 Acquisition parameters PulseSeq *tfl3d1 Protocol t1_3d_mpr_sag PhEncDir ROW EchoNo 0 FlipAngle 15 EchoTime 3.19 InversionTime 1100 RepetitionTime 2730 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 128 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos -91.5886 131.5105 125.9759 VolRes 0.5000 0.5000 1.3300 VolDim 512 512 128 Vc 0.0297 -0.9996 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -0.9996 -0.0297 0.0000 VolCenter -172.8739 1.0416 -2.0241 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2730.00, TE=3.19, TI=1100.00, flip angle=15.00 i_ras = (0.0296663, -0.99956, 0) j_ras = (-0, -0, -1) k_ras = (-0.99956, -0.0296663, 0) writing to /labdata/lab-data/testinge/testE0000002/mri/orig/001.mgz... Scan info from nICE: Manufacure's model name (0008,1090): Symphony Scanning sequenece (0018,0020): IR\GR Scanning variant (0018,0021): SP\MP Scan options (0018,0022): IR Acquisition type (0018,0023): 3D Scan (Sequence) Name (0018,0024): *tfl3d1 Protocol Name (0018,1030): t1_3d_mpr_sag Repetition time, TR (ms)(0018,0080): 2730.0 Echo time, TE (ms) (0018,0081): 3.2 Inversion time, TI (ms) (0018,0082): 1100.000 Flip angle (deg) (0018,1314): 15 Pixel spacing X (mm) (0028,0030): 0.5000 Pixel spacing Y (mm) (0028,0030): 0.5000 Slice thickness (mm) (0018,0050): 1.3300 Slice spacing or gap (mm) (0018,0088): 0.0000 FoV (freq*phase, mm): 256.0000 * 256.0000 Rect. FoV percentage: 100.0 No of PE steps (0018,0089): 192 Turbo Factor (ETL) (0018,0091): 1 Scan Percentage (0018,0093): 75.0 Pixel Bandwidth (Hz) (0018,0095): 190.0 Number of averages (0018,0083): 1 Recon resolution (Rows) (0028,0010): 512 Recon resolution (Columns) (0028,0011): 512 Image matrix size (X * Y pixels): 512 * 512 Scan number (0020,0012): 1 Image (instance) number (0020,0013): 128 Series number (0020,0011): 2

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