Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

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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Re: [Freesurfer] Faster and Parallel recon-all
by skenny＠uchicago.edu 23 Mar '06

23 Mar '06

hi there, i'm actually working on parallelizing recon-all on a grid...i *think* the script won't work all the way thru bcs calling recon-all with the -normalization2 flag is supposed to call both mri_normalize AND mri_mask (according to the DevTable); but it looks as if the recon-all script only calls mri_normalize with that flag...this means mri_mask is never called and brain.finalsurfs.mgz is not produced...so when you get to -finalsurfs it can't find the file...alas i just changed the recon-all script to call mri_mask when it gets the -norm2 flag...this seems to have worked. sarah ---- Original message ---- >Date: Wed, 22 Mar 2006 18:09:11 -0500 >From: Daniel Goldenholz <daniel(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Faster and Parallel recon-all >To: "Goradia, Dhruman D" <goradiadd(a)upmc.edu> >Cc: freesurfer(a)nmr.mgh.harvard.edu > >Hi again, > >I have totally revamped the script in light of the fact that recon-all >-notify did not do what I thought it did at all! >The new and improved (version 1.02) super-recon is quite a bit fancier. >Now, I leave all notifcations and waiting and emailing to super-recon >itself, so that recon-all assumptions are reduced. > >If you want to run a complete recon-all -all but have the hemisphere >parts run in parallel, you run a command like this one: >super_recon all $SUBJECTS_DIR $SUBJECT /space/dicom/file1 >/space/dicom/file2 my_email(a)wherever.nmr.com > >Using this new and improved command, if you have a cluster with daul >processors, then you should be able to run multiple >subjects faster than a standard recon-all command. > > >The script in "all" mode will run the same stuff as recon- all -all. >If you wish to run a subset of the full set of commands, you can simply >comment out a specific line you don't want. >There are also several other ways to call the script now, since in >reality it calls itself recursively with different options. > >Hopefully this one will do what the original one intended to do. >Good luck, >Daniel > >Goradia, Dhruman D wrote: > >>Hi Daniel, >>The script is ok but it still does not make it to the end. As the script >>is designed to send me an email at the end of the last step, I got an >>email within 15 min after I executed the script saying that "recon-all >>14777 finished with errors at Tue Mar 21 18:46:15 EST 2006". However it >>went on the complete the "gcareg" step. >>I have attached the status and log files for your reference. If you get >>a chance have a look at it. I believe this problem is not due to >>super-recon script but due to recon-all script. Please let me know. >>I am very interested in the super-recon script, as it takes about 30 hrs >>to process 1 scan currently. >>-Dhruman >> >>-----Original Message----- >>From: Daniel Goldenholz [mailto:daniel@nmr.mgh.harvard.edu] >>Sent: Tuesday 21 March 2006 17:09 >>To: Goradia, Dhruman D >>Cc: freesurfer(a)nmr.mgh.harvard.edu >>Subject: Re: [Freesurfer] Faster and Parallel recon-all >> >>Dhruman >> >>Thanks for catching that. Spelling was never my strong point. I have >>corrected the script on my website. >> >>As for you second problem, did you properly remove the waitfor >>step1-00.done from the motion correction step, since you >>say you skipped step1-00, i.e. the invol step? I mention this in a >>comment near the top of the script. >> >>D >> >>Goradia, Dhruman D wrote: >> >> >> >>>Hi Daniel, >>>I was having a second look at the script and apparently the script is >>>fine with a small spelling error. The STAT variable which is set at 3 >>>different instances has spelling error in "scripts" where "t" is >>>missing. >>>Once this was corrected the script is fine but it's still not working. >>>It initiates all the processes and then just sits idle. After waiting >>>for half an hour it still does not make step1-00.done (I start directly >>>with motion cor) keeping all the other processes waiting. I am still >>>probing into this. If you can think of something that might be of help >>>then let me know. >>>-Dhruman >>> >>>-----Original Message----- >>>From: Daniel Goldenholz [mailto:danielg@bu.edu] >>>Sent: Tuesday 21 March 2006 11:25 >>>To: Goradia, Dhruman D >>>Subject: Re: [Freesurfer] Faster and Parallel recon-all >>> >>>Dhruman >>> >>>That's confusing. I think you should take one line of executable code >>> >>> >>>from your script that produces that behavior and then email it to the >> >> >>>freesurfer list. >>> >>>It sounds to me like the recon-all script ASSUMES that the log file >>>exists if you specify a name. I thought it actually creates one first, >>>but I could have been mistaken there, and if so I will need to add a >>> >>> >>few >> >> >>>extra lines of code. >>>PLEASE follow up on this. It will help others. >>> >>>The other thing to try is to create a text file first, such as like >>>this: >>>echo "#Starting recon-all manually..." > >>>/Applications/freesurfer/subjects/ddg6/scripts/recon-all- status.log >>> >>>and then see if my script is ok. >>> >>>Keep me posted. >>> >>>D >>> >>>Goradia, Dhruman D wrote: >>> >>> >>> >>> >>> >>>>Hi Daniel, >>>>I tried to use the script super-recon on mac OX S using bash shell. I >>>>made the necessary changes to make it operable in bash. However when I >>>>run the script its gives me the following error: >>>> >>>>Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon- all-status.l >>>> >>>> >>o >> >> >>>> >>>> >>>> >>>> >>>g >>> >>> >>> >>> >>>>:not a file or directory. >>>> >>>>I tried to run the first 3 steps of the script (motioncor, >>>>nuintensitycor, talairach) and it gives the above error. However if I >>>>remove the log and status flags, the first 3 steps executes properly. >>>> >>>> >>>> >>>> >>>Do >>> >>> >>> >>> >>>>you have any idea why? Do you see any problem if I delete the log and >>>>status flags from the whole script and use it? >>>>-Dhruman >>>> >>>>-----Original Message----- >>>>From: freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Daniel >>>>Goldenholz >>>>Sent: Thursday 16 March 2006 15:17 >>>>Cc: Freesurfer Mailing List; Nick Schmansky >>>>Subject: Re: [Freesurfer] Faster and Parallel recon-all >>>> >>>>Ah. Silly me, I didn't notice the -log and -status options. Thanks >>>> >>>> >>>> >>>> >>>Nick. >>> >>> >>> >>> >>>>I have now included those into my super-recon script as well. Problem >>>>solved. >>>> >>>>(if you have seen my script already, you may need to hit RELOAD on >>>> >>>> >>your >> >> >>>> >>>> >>>> >>>> >>> >>> >>> >>> >>>>browser to see the new version) >>>>Daniel >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>>Nick Schmansky wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>The script looks good. The one thing it needs though is for the >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>right >>>> >>>> >>>> >>>> >>>> >>>> >>>>>>and left hemi steps to log to separate files, otherwise output to >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>recon- >>>> >>>> >>>> >>>> >>>> >>>> >>>>>>all.log will be interleaved, making debugging impossible. >>>>>> >>>>>>On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>Ooops. I sent the below with the wrong subject tag. Here it is >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>again: >>>> >>>> >>>> >>>> >>>> >>>> >>>>>>>Daniel Goldenholz wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>>Freesurfers >>>>>>>> >>>>>>>>I was hoping someone else would do this, but well, it seems that >>>>>>>> >>>>>>>> >>no >> >> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>>> >>>> >>>> >>>>>>>>one did. So I went ahead and made this myself. >>>>>>>>Amusingly, I don't NEED to reconstruct any brains right now, so I >>>>>>>>don't have anything to test this out with. >>>>>>>>Please someone try it, and let me know if it is helpful. >>>>>>>> >>>>>>>>What I did was write a script that runs each and every part of the >>>>>>>> >>>>>>>> >> >> >> >>>>>>>>recon-all -all stream, one command at a time. (based on the NEW >>>>>>>>version 3 stream). >>>>>>>>Each one is loaded with -waitfor and -notify so that the >>>>>>>> >>>>>>>> >>dependency >> >> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>>> >>>> >>>> >>>>>>>>structure is intact. >>>>>>>>However, ALL of the commands start running in the background! If >>>>>>>>you have a 2 more processor system, then recon-all should complete >>>>>>>> >>>>>>>> >> >> >> >>>>>>>>in about HALF the time as it usually does, since all the >>>>>>>> >>>>>>>> >>hemisphere >> >> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>>> >>>> >>>> >>>>>>>>specific stuff can be done in parallel. >>>>>>>>At the completion of each hemipshere, it will email you. >>>>>>>> >>>>>>>>I included a command for each minute step so that people can >>>>>>>> >>>>>>>> >>easily >> >> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>>> >>>> >>>> >>>>>>>>fiddle with options and commands and so forth. >>>>>>>> >>>>>>>>Obviously, if you run recon-all -autoreon1, then you can then run >>>>>>>>my script (after deleting the step1-??.done lines). >>>>>>>>If you run recon-all -autorecon2, then you can run my script >>>>>>>> >>>>>>>> >>(after >> >> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>>> >>>> >>>> >>>>>>>>deleting the step1-??.done and step2-??.done lines) >>>>>>>>And so forth. >>>>>>>> >>>>>>>>To see the script, go here: >>>>>>>>http://www.nmr.mgh.harvard.edu/~daniel >>>>>>>>click on fMRI scripts >>>>>>>>click on super-recon >>>>>>>> >>>>>>>>Enjoy, and PLEASE email me if you use this. If there are >>>>>>>>corrections I can easily post them. >>>>>>>>Daniel >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>>> >>>> >>>> >>>_______________________________________________ >>>Freesurfer mailing list >>>Freesurfer(a)nmr.mgh.harvard.edu >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe r >>> >>> >>> >>> > >-- >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 > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mri_convert problems
by karsten.specht＠email.de 23 Mar '06

23 Mar '06

Hi Inge, > 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? The log say's that it has found 130 dcm files, which is two files too much for a 128slice sequence, as nICE is saying. So, perhaps there is something in the folder, which should not be there, even though mri_convert also detectes that the sequence had originally 128 slices, but this might have produced this offset in the images. How does the volume look likes, when you are looding it into nICE? Best reagrds, Karsten -- ------------------------------------------------------------- Karsten Specht, PhD Department of Biological and Medical Psychology & National Competence Centre for functional MRI University of Bergen Jonas Lies vei 91 5009 Bergen Norway Tel.: +47-555-86279 Fax: +47-555-89872 karsten.specht(a)psybp.uib.no http://fmri.uib.no/

1 0

--conform option
by Pellegrini, Stefano (NIH/NINDS) [F] 23 Mar '06

23 Mar '06

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

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RE: [Freesurfer] Faster and Parallel recon-all
by Goradia, Dhruman D 22 Mar '06

22 Mar '06

Hi Daniel, The script is ok but it still does not make it to the end. As the script is designed to send me an email at the end of the last step, I got an email within 15 min after I executed the script saying that "recon-all 14777 finished with errors at Tue Mar 21 18:46:15 EST 2006". However it went on the complete the "gcareg" step. I have attached the status and log files for your reference. If you get a chance have a look at it. I believe this problem is not due to super-recon script but due to recon-all script. Please let me know. I am very interested in the super-recon script, as it takes about 30 hrs to process 1 scan currently. -Dhruman -----Original Message----- From: Daniel Goldenholz [mailto:daniel@nmr.mgh.harvard.edu] Sent: Tuesday 21 March 2006 17:09 To: Goradia, Dhruman D Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Faster and Parallel recon-all Dhruman Thanks for catching that. Spelling was never my strong point. I have corrected the script on my website. As for you second problem, did you properly remove the waitfor step1-00.done from the motion correction step, since you say you skipped step1-00, i.e. the invol step? I mention this in a comment near the top of the script. D Goradia, Dhruman D wrote: >Hi Daniel, >I was having a second look at the script and apparently the script is >fine with a small spelling error. The STAT variable which is set at 3 >different instances has spelling error in "scripts" where "t" is >missing. >Once this was corrected the script is fine but it's still not working. >It initiates all the processes and then just sits idle. After waiting >for half an hour it still does not make step1-00.done (I start directly >with motion cor) keeping all the other processes waiting. I am still >probing into this. If you can think of something that might be of help >then let me know. >-Dhruman > >-----Original Message----- >From: Daniel Goldenholz [mailto:danielg@bu.edu] >Sent: Tuesday 21 March 2006 11:25 >To: Goradia, Dhruman D >Subject: Re: [Freesurfer] Faster and Parallel recon-all > >Dhruman > >That's confusing. I think you should take one line of executable code >from your script that produces that behavior and then email it to the >freesurfer list. > >It sounds to me like the recon-all script ASSUMES that the log file >exists if you specify a name. I thought it actually creates one first, >but I could have been mistaken there, and if so I will need to add a few > >extra lines of code. >PLEASE follow up on this. It will help others. > >The other thing to try is to create a text file first, such as like >this: >echo "#Starting recon-all manually..." > >/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.log > >and then see if my script is ok. > >Keep me posted. > >D > >Goradia, Dhruman D wrote: > > > >>Hi Daniel, >>I tried to use the script super-recon on mac OX S using bash shell. I >>made the necessary changes to make it operable in bash. However when I >>run the script its gives me the following error: >> >>Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.l o >> >> >g > > >>:not a file or directory. >> >>I tried to run the first 3 steps of the script (motioncor, >>nuintensitycor, talairach) and it gives the above error. However if I >>remove the log and status flags, the first 3 steps executes properly. >> >> >Do > > >>you have any idea why? Do you see any problem if I delete the log and >>status flags from the whole script and use it? >>-Dhruman >> >>-----Original Message----- >>From: freesurfer-bounces(a)nmr.mgh.harvard.edu >>[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Daniel >>Goldenholz >>Sent: Thursday 16 March 2006 15:17 >>Cc: Freesurfer Mailing List; Nick Schmansky >>Subject: Re: [Freesurfer] Faster and Parallel recon-all >> >>Ah. Silly me, I didn't notice the -log and -status options. Thanks >> >> >Nick. > > >>I have now included those into my super-recon script as well. Problem >>solved. >> >>(if you have seen my script already, you may need to hit RELOAD on your >> >> > > > >>browser to see the new version) >>Daniel >> >> >> >> >> >>>Nick Schmansky wrote: >>> >>> >>> >>> >>> >>>>The script looks good. The one thing it needs though is for the >>>> >>>> >>>> >>>> >>right >> >> >> >> >>>>and left hemi steps to log to separate files, otherwise output to >>>> >>>> >>>> >>>> >>recon- >> >> >> >> >>>>all.log will be interleaved, making debugging impossible. >>>> >>>>On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote: >>>> >>>> >>>> >>>> >>>> >>>> >>>>>Ooops. I sent the below with the wrong subject tag. Here it is >>>>> >>>>> >>>>> >>>>> >>again: >> >> >> >> >>>>>Daniel Goldenholz wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Freesurfers >>>>>> >>>>>>I was hoping someone else would do this, but well, it seems that no >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>one did. So I went ahead and made this myself. >>>>>>Amusingly, I don't NEED to reconstruct any brains right now, so I >>>>>>don't have anything to test this out with. >>>>>>Please someone try it, and let me know if it is helpful. >>>>>> >>>>>>What I did was write a script that runs each and every part of the >>>>>>recon-all -all stream, one command at a time. (based on the NEW >>>>>>version 3 stream). >>>>>>Each one is loaded with -waitfor and -notify so that the dependency >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>structure is intact. >>>>>>However, ALL of the commands start running in the background! If >>>>>>you have a 2 more processor system, then recon-all should complete >>>>>>in about HALF the time as it usually does, since all the hemisphere >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>specific stuff can be done in parallel. >>>>>>At the completion of each hemipshere, it will email you. >>>>>> >>>>>>I included a command for each minute step so that people can easily >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>fiddle with options and commands and so forth. >>>>>> >>>>>>Obviously, if you run recon-all -autoreon1, then you can then run >>>>>>my script (after deleting the step1-??.done lines). >>>>>>If you run recon-all -autorecon2, then you can run my script (after >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> >>>>>>deleting the step1-??.done and step2-??.done lines) >>>>>>And so forth. >>>>>> >>>>>>To see the script, go here: >>>>>>http://www.nmr.mgh.harvard.edu/~daniel >>>>>>click on fMRI scripts >>>>>>click on super-recon >>>>>> >>>>>>Enjoy, and PLEASE email me if you use this. If there are >>>>>>corrections I can easily post them. >>>>>>Daniel >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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