Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] Paired analysis results into table?
by Braber, A. den 01 Sep '11

01 Sep '11

Hi, I just performed a paired analysis on my twin data. I am interested in the difference in cortical thickness between males and females, and have to run a paired analysis since the males and females in my sample are related (because they are twins). No covariate (such as age) has been included in the mri_glmfit yet, so I only have 1 contrast (mean.mtx = 1, meaning in my case males greater than females). After running the mri_glmfit I viewed my results using ' tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay $SUBJECTS_DIR/ sig.mgh'. Thereafter I corrected my results using FDR-correction, under View->Configure->Overlay->set threshold using FDR, rate 0.05 (so I did not perform a clusterwise correction for multiple comparison). Tksurfer than gives me a really nice overview of the significant results (FDR-corrected) of my paired analysis. I wondered whether there is a tool to export these results into a table (just like it's possible with aparc2table), so I get an overview of, for example, T-statistics, p-value and vertex number, for the observed significant clusters (or vertex with the highest T-value within an observed cluster). Is this possible? I have searched for a command to do this, but unfortunately I couldn't find it. Could you please help me? Thanks in advance. Anouk den Braber

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ANOVA(analysis of variance)
by ZhiLiangLong 01 Sep '11

01 Sep '11

Hi all: Is there a way that can perform a test to compare the difference of cortical thickness between groups (at least three) using ANOVA (analysis of variance) in FS? If it is how can i do that? Any suggestions will be appreciative

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Subject: Research position (PhD) in translational developmental neuroscience (with a focus on eating disorders)
by stefan＠nmr.mgh.harvard.edu 01 Sep '11

01 Sep '11

Research position (PhD) in translational developmental neuroscience (with a focus on eating disorders) at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Dresden University of Technology, Germany PLEASE REPOST FOR INTERESTED PARTIES Job Description: The Department of Child and Adolescent Psychiatry, Dresden University of Technology, Germany invites applications for a research position (PhD) in neuroimaging of eating disorders (ED). We are interested in cognitive control, reward system and the processing of emotions in patients with anorexia nervosa. This is a full time position within the Translational Developmental Neuroscience Group. Some of the work will be carried out in close collaboration with scientists at the Massachusetts General Hospital/ Harvard Medical School (Boston, USA). Responsibilities will include the coordination of our ongoing clinical study and the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner and data collected includes high-quality structural, diffusion, and functional MRI data. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, physiological and endocrinological information. The successful applicant will work in a team of young investigators and also be responsible to supervise interns and medical students working in the project. Applicants for the position must have completed (a) a Bachelor, Master or Diploma degree in a relevant field (Psychology, Neurosciences or Medicine; if you have additional qualifications a degree in Biology, Biomedicine, Biophysics, Computer Science or Electrical Engineering may also be sufficient) and (b) participated in research activities within the past years. Experience in computer programming (Linux/Unix shell scripting, C++ and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer), advanced statistical analyses is of advantage but not a precondition. The successful applicant will join a multidisciplinary team of researchers and clinicians and will receive further training in psychometric and endocrinological techniques and the application of analysis tools for neuroimaging data. Psychologists or physicians who wish to advance in their clinical training may be able to dedicate some amount of their time to work with patients. The position is available for a start date as soon as October 15th 2011 (to be confirmed). Review of applications will begin immediately and will continue until the position is filled. The position is guaranteed for one year with the possibility of renewal after positive evaluation. Salary will be consistent with levels in accordance with the German Research Foundation (50% TV-L: E 13). Compensation includes health insurance, and vacation time. To apply you can use our online portal (http://www.uniklinikum-dresden.de/bildung-und-karriere/stellenangebote/wiss…) The application should include a cover letter detailing professional objectives and interests, CV (with grades), and the names and email addresses of two references. The application can be written in German or English. Applications from many disciplines may be considered. The position is open to qualified international applicants but the knowledge of some German is necessary since the position includes the coordination of an ongoing clinical study. Applicants with a disability will be given preference in the selection process. Stefan Ehrlich Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus Dresden an der TU Dresden E-Mail: KJPChefsekretariat(a)uniklinikum-dresden.de Please refer to our homepage: http://www.kjp-dresden.de/en/Eating-disorders, http://www.kjp-dresden.de/en/Schizophrenia and http://kjp-dresden.de/de/Publikationsliste-Prof-Dr-S-Ehrlich for more detailed information.

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Re: [Freesurfer] integrating FSL and Freesurfer
by Douglas N Greve 31 Aug '11

31 Aug '11

noam Schneck wrote: > Hi Doug > > Here are more detailed versions of my first two questions. > > 1) I used tkmedit to look at the mean_func produced by a gfeat > analysis of one subject's three functional runs overlayed onto the > anatomical image produced by recon-all on that same > subject(bert/mri/orig.mgz). The registration matrix I used was the > anat2std.dat that was produced by running reg-feat2anat on all three > of the feat analyses from the individual runs. When I did this I saw > that the mean_func image was outside the boundaries of the anatomical > image. Correspondingly, when I overlayed the zstat.nii.gz from the > gfeat analysis onto the anatomical image I had activation outside of > the anatomical image brain. What was the command line? > > 2) Originally, I ran BBR on a subject that I had run Recon-all for. > I used BBR to register the example_func.nii.gz to the > bert/mri/orig.mgz. I had BBR output an fsl.mat. I then used ApplyXFM > in fsl to apply BBR's fsl.mat to register the example_func.nii.gz onto > a T1 image that had been created by converting bert/mri/brainmask.mgz > into niftii with mri_convert. I tried it again, this time converting > the orig.mgz to niftii. In both cases the example_func in T1 space > image produced by ApplyXFM is rotated about 90 degrees and also > inverted. This is viewed in fslview, I have attached a screenshot. > The corresponding T1 images created by mri_convert are not. What can > I do to allow me to use BBR's fsl.mat within ApplyXFM? > > Here is the header info for the T2*_T1 image attached to this email. > sizeof_hdr 348 > data_type FLOAT32 > dim0 3 > dim1 256 > dim2 256 > dim3 256 > dim4 1 > dim5 1 > dim6 1 > dim7 1 > vox_units mm > time_units s > datatype 16 > nbyper 4 > bitpix 32 > pixdim0 0.0000000000 > pixdim1 1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.0000000000 > pixdim4 1.5000000000 > pixdim5 1.0000000000 > pixdim6 1.0000000000 > pixdim7 1.0000000000 > vox_offset 352 > cal_max 0.0000 > cal_min 0.0000 > scl_slope 0.000000 > scl_inter 0.000000 > phase_dim 0 > freq_dim 0 > slice_dim 0 > slice_name Unknown > slice_code 0 > slice_start 0 > slice_end 0 > slice_duration 0.000000 > time_offset 0.000000 > intent Unknown > intent_code 0 > intent_name > intent_p1 0.000000 > intent_p2 0.000000 > intent_p3 0.000000 > qform_name Scanner Anat > qform_code 1 > qto_xyz:1 -1.000000 -0.000000 -0.000000 128.678986 > qto_xyz:2 -0.000000 0.000000 1.000000 -100.598366 > qto_xyz:3 0.000000 -1.000000 0.000000 143.524200 > qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > qform_xorient Right-to-Left > qform_yorient Superior-to-Inferior > qform_zorient Posterior-to-Anterior > sform_name Scanner Anat > sform_code 1 > sto_xyz:1 -1.000000 -0.000000 0.000000 128.678986 > sto_xyz:2 -0.000000 -0.000000 1.000000 -100.598366 > sto_xyz:3 -0.000000 -1.000000 0.000000 143.524200 > sto_xyz:4 0.000000 0.000000 0.000000 1.000000 > sform_xorient Right-to-Left > sform_yorient Superior-to-Inferior > sform_zorient Posterior-to-Anterior > file_type NIFTI-1+ > file_code 1 > descrip FreeSurfer Jun 18 2008 > aux_file > > > Thank you, > Noam > > On Mon, Aug 29, 2011 at 1:16 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Noam, > > > noam Schneck wrote: > > Hi, > > I am trying to use reg-feat2anat to register my Feat analyses > to anatomical images and running into a number of problems. > 1) When I check the registration of the mean_func to the > anatomical in tkregister2 it looks fine. But when I overlay > the fsl statmaps onto the anatomical brain they extend outside > of boundaries of the anatomical brain. > > Need more detail. What command are you using to visualize? > > > 2) Also, before using reg-feat2anat. I was trying to do the > EPI_2_structural registration in FLIRT with the fsl.mat > produced by BBR. When I try this the registered image is > rotated 90 degrees from the original image. Why does that happen? > > More detail needed. What program did you run? What visualization > tool? This will align the anatomical in the conformed space to the > EPI, so make sure you're using the right anatomical. > > > 3) I also noticed that if I look at the header information for > an image in fslhd and mri_info the orientations are flipped. > If the fslhd orientation is RAS it will be LPI in mri_info. > Could this be related to what is happening in question (2)? > > Need more detail. What images are you looking at? > > In general, you have to tell us specifically what you are doing. > It's going to be very hard to help with vague descriptions. > doug > > > Best, > Noam > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > ------------------------------------------------------------------------ > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] : Error with dt_recon
by Douglas N Greve 31 Aug '11

31 Aug '11

you need to find out what values need to go into you bvals and bvects file to match what you acquired. I don't know what you acquired so I can't help you. Sometimes the bval/bvect files dont include a bval=0 acquisition at the beginning, so check that first Antonella Kis wrote: > Hi Doug, > > I know that but how can I correct this? > > Thanks, > AK > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, August 31, 2011 3:36 PM > *Subject:* Re: [Freesurfer] : Error with dt_recon > > your data have 17 frames, but you bvals and bvects only have 16 values. > > Antonella Kis wrote: > > Dear Doug, > > > > I used the mentioned bvals and bvecs but I am getting the following > error: > > > > Loading y from /usr/local/freesurfer/NPI001/DTI_15/dwi-ec.nii > > Using DTI > > Loading BValues from bvals.dat > > Found 16 bvalues > > Loading BVectors from bvecs.dat > > Found 16 bvectorss > > Detected BVec file as FSL formatted > > Saving design matrix to /usr/local/freesurfer/NPI001/DTI_15/Xg.dat > > Normalized matrix condition is 74.3726 > > Matrix condition is 6.03077e+06 > > Pruning voxels by thr: 0.000000 > > Found 2731724 voxels in mask > > Saving mask to /usr/local/freesurfer/NPI001/DTI_15/mask.nii > > search space = 4182952.500000 > > ERROR: dimension mismatch between y and X. > > y has 17 inputs, X has 16 rows. > > Is there a way to fix this error? > > > > Thank you. > > AK > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer > > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, August 31, 2011 3:00 PM > > *Subject:* Re: [Freesurfer] : Error with dt_recon > > > > If they meet the requirements outlined in the help section (run with > > --help). > > > > Antonella Kis wrote: > > > Dear Doug, > > > > > > I can get this values if I convert the dicom files with MRIcron. Can I > > > use this values? > > > > > > Thanks. > > > Antonella > > > > > > PS> Why when I ran the dt_recon I didn't get the fa.nii, adc.nii and > > > some more file? Is thsi because I didn't have the bvects and bvals? > > > > > > > ------------------------------------------------------------------------ > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>; > > freesurfer > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > *Sent:* Wednesday, August 31, 2011 2:35 PM > > > *Subject:* Re: [Freesurfer] : Error with dt_recon > > > > > > It does not always work to extract them from the dicom. You should > talk > > > to whoever set up your scans to get the bvals and bvects. > > > doug > > > > > > Antonella Kis wrote: > > > > Hi Doug, > > > > > > > > Thanks again. From where I take the bvals and bvects. I was reading > > > > that if my DICOM files were acquired using a Siemens scanner, then > > > > this information can be extracted from the DICOM headers but I don't > > > > know how to do it. > > > > > > > > > > > > Please help. > > > > > > > > Many thanks. > > > > AK > > > > > > ------------------------------------------------------------------------ > > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > *To:* Antonella Kis <atorok9(a)yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>> > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>>; > > > freesurfer > > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > *Sent:* Wednesday, August 31, 2011 2:11 PM > > > > *Subject:* Re: [Freesurfer] : Error with dt_recon > > > > > > > > > > > > That's almost right. Just specify the subject name and not the full > > > > path. Also, you will need to supply bvals and bvects > > > > dt_recon --i DTI_15.nii.gz --s NPI001 --o > > > > /usr/local/freesurfer/NPI001/DTI_15 > > > > > > > > > > > > > > > > Antonella Kis wrote: > > > > > Hi Doug, > > > > > > > > > > Thanks again for helping. So my question is then: I will pass > > for --i > > > > > (the input data) the .nii.gz file from the DTI data and the it > > is OK > > > > > to use for the --s which defines the file of the structural > recon a > > > > > file called NPI001 where I have 10 files after recon-all (bem, > > label, > > > > > mri, surf, stats, etc)? In other words if I will set-up: > > > > > > > > > > setenv FREESURFER_HOME /usr/local/freesurfer > > > > > setenv SUBJECTS_DIR $FREESURFER_HOME > > > > > > > > > > and since my files are in /usr/local/freesurfer/NPI001 I am then > > > doing: > > > > > > > > > > cd /usr/local/freesurfer/NPI001 > > > > > > > > > > Here I have the pre-processed files after recon-all and a file > > called > > > > > DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can > > > run: > > > > > > > > > > dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o > > > > > /usr/local/freesurfer/NPI001/DTI_15 > > > > > > > > > > Is this right? > > > > > > > > > > I will try by the time you answer but please let me know if > you have > > > > > any objection and/or advise. > > > > > > > > > > Many thanks, > > > > > AK > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> > > > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>> > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>>>; > > > > freesurfer > > > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > *Sent:* Wednesday, August 31, 2011 1:49 PM > > > > > *Subject:* Re: [Freesurfer]: Error with dt_recon > > > > > > > > > > If you pass it dicom, it will try to extract the bvalues, which is > > > > > where it is failing. > > > > > doug > > > > > > > > > > Antonella Kis wrote: > > > > > > Dear Doug, > > > > > > > > > > > > Sorry but I still have a question about this error: > > > > > > I understood that dt_recon it takes original dicom images as > input > > > > > and it generates multiple NIFTI volumes that will be used in later > > > > > steps.So why I need to use the NIFTI as input? > > > > > > > > > > > > Thnak you. > > > > > > AK > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>>> > > > > > > *To:* Antonella Kis <atorok9(a)yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>> > > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>> > > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>> > > > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>> > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>> > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>>>> > > > > > > *Cc:* "fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>>>" <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> > > > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>>>>; > > > "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>" > > > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>> > > > > > > *Sent:* Tuesday, August 30, 2011 3:51 PM > > > > > > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > > > > > > > > > > > It's looking for the values in the dicom file (which > > apparently does > > > > > not have them). Convert the dicom to nifit, then use the nifti as > > > > > input, then pass files with bvals and bvects on the command line. > > > > > > doug > > > > > > > > > > > > Antonella Kis wrote: > > > > > > > > > > > > > > > > > > > > > Dear Bruce: > > > > > > > > > > > > > > I am running the dt_recon: > > > > > > > # setenv FREESURFER_HOME /usr/local/freesurfer # > setenv > > > > > SUBJECTS_DIR $FREESURFER_HOME > > > > > > > # cd /usr/local/freesurfer/NPI001 > > > > > > > # dt_recon --i > > > > > > > > > > > > > > > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > > > > > > > > > > > > > > > --s /usr/local/freesurfer/NPI001 --o > > /usr/local/freesurfer/NPI001/dti > > > > > > > > > > > > > > > > > > > > > and I am getting the following error: > > > > > > > > > > > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > > > > > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > > > > > > > > > > > Can you please give me a hint? > > > > > > > > > > > > > > Thank you. > > > > > > > AK > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>> > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > > > > > MGH-NMR Center > > > > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> > > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>> > > > > > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> > > > > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Douglas N. Greve, Ph.D. > > > > MGH-NMR Center > > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > Phone Number: 617-724-2358 > > > > Fax: 617-726-7422 > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

Re: [Freesurfer] : Error with dt_recon
by Douglas N Greve 31 Aug '11

31 Aug '11

If they meet the requirements outlined in the help section (run with --help). Antonella Kis wrote: > Dear Doug, > > I can get this values if I convert the dicom files with MRIcron. Can I > use this values? > > Thanks. > Antonella > > PS> Why when I ran the dt_recon I didn't get the fa.nii, adc.nii and > some more file? Is thsi because I didn't have the bvects and bvals? > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, August 31, 2011 2:35 PM > *Subject:* Re: [Freesurfer] : Error with dt_recon > > It does not always work to extract them from the dicom. You should talk > to whoever set up your scans to get the bvals and bvects. > doug > > Antonella Kis wrote: > > Hi Doug, > > > > Thanks again. From where I take the bvals and bvects. I was reading > > that if my DICOM files were acquired using a Siemens scanner, then > > this information can be extracted from the DICOM headers but I don't > > know how to do it. > > > > > > Please help. > > > > Many thanks. > > AK > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer > > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, August 31, 2011 2:11 PM > > *Subject:* Re: [Freesurfer] : Error with dt_recon > > > > > > That's almost right. Just specify the subject name and not the full > > path. Also, you will need to supply bvals and bvects > > dt_recon --i DTI_15.nii.gz --s NPI001 --o > > /usr/local/freesurfer/NPI001/DTI_15 > > > > > > > > Antonella Kis wrote: > > > Hi Doug, > > > > > > Thanks again for helping. So my question is then: I will pass for --i > > > (the input data) the .nii.gz file from the DTI data and the it is OK > > > to use for the --s which defines the file of the structural recon a > > > file called NPI001 where I have 10 files after recon-all (bem, label, > > > mri, surf, stats, etc)? In other words if I will set-up: > > > > > > setenv FREESURFER_HOME /usr/local/freesurfer > > > setenv SUBJECTS_DIR $FREESURFER_HOME > > > > > > and since my files are in /usr/local/freesurfer/NPI001 I am then > doing: > > > > > > cd /usr/local/freesurfer/NPI001 > > > > > > Here I have the pre-processed files after recon-all and a file called > > > DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can > run: > > > > > > dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o > > > /usr/local/freesurfer/NPI001/DTI_15 > > > > > > Is this right? > > > > > > I will try by the time you answer but please let me know if you have > > > any objection and/or advise. > > > > > > Many thanks, > > > AK > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>; > > freesurfer > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > *Sent:* Wednesday, August 31, 2011 1:49 PM > > > *Subject:* Re: [Freesurfer]: Error with dt_recon > > > > > > If you pass it dicom, it will try to extract the bvalues, which is > > > where it is failing. > > > doug > > > > > > Antonella Kis wrote: > > > > Dear Doug, > > > > > > > > Sorry but I still have a question about this error: > > > > I understood that dt_recon it takes original dicom images as input > > > and it generates multiple NIFTI volumes that will be used in later > > > steps.So why I need to use the NIFTI as input? > > > > > > > > Thnak you. > > > > AK > > > > > > > > > > ------------------------------------------------------------------------ > > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > *To:* Antonella Kis <atorok9(a)yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>> > > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>> > > > > *Cc:* "fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>" <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>>; > "freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>" > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > *Sent:* Tuesday, August 30, 2011 3:51 PM > > > > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > > > > > > > It's looking for the values in the dicom file (which apparently does > > > not have them). Convert the dicom to nifit, then use the nifti as > > > input, then pass files with bvals and bvects on the command line. > > > > doug > > > > > > > > Antonella Kis wrote: > > > > > > > > > > > > > > > Dear Bruce: > > > > > > > > > > I am running the dt_recon: > > > > > # setenv FREESURFER_HOME /usr/local/freesurfer # setenv > > > SUBJECTS_DIR $FREESURFER_HOME > > > > > # cd /usr/local/freesurfer/NPI001 > > > > > # dt_recon --i > > > > > > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > > > > > > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti > > > > > > > > > > > > > > > and I am getting the following error: > > > > > > > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > > > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > > > > > > > Can you please give me a hint? > > > > > > > > > > Thank you. > > > > > AK > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- Douglas N. Greve, Ph.D. > > > > MGH-NMR Center > > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 2

Re: [Freesurfer] : Error with dt_recon
by Douglas N Greve 31 Aug '11

31 Aug '11

It does not always work to extract them from the dicom. You should talk to whoever set up your scans to get the bvals and bvects. doug Antonella Kis wrote: > Hi Doug, > > Thanks again. From where I take the bvals and bvects. I was reading > that if my DICOM files were acquired using a Siemens scanner, then > this information can be extracted from the DICOM headers but I don't > know how to do it. > > > Please help. > > Many thanks. > AK > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, August 31, 2011 2:11 PM > *Subject:* Re: [Freesurfer] : Error with dt_recon > > > That's almost right. Just specify the subject name and not the full > path. Also, you will need to supply bvals and bvects > dt_recon --i DTI_15.nii.gz --s NPI001 --o > /usr/local/freesurfer/NPI001/DTI_15 > > > > Antonella Kis wrote: > > Hi Doug, > > > > Thanks again for helping. So my question is then: I will pass for --i > > (the input data) the .nii.gz file from the DTI data and the it is OK > > to use for the --s which defines the file of the structural recon a > > file called NPI001 where I have 10 files after recon-all (bem, label, > > mri, surf, stats, etc)? In other words if I will set-up: > > > > setenv FREESURFER_HOME /usr/local/freesurfer > > setenv SUBJECTS_DIR $FREESURFER_HOME > > > > and since my files are in /usr/local/freesurfer/NPI001 I am then doing: > > > > cd /usr/local/freesurfer/NPI001 > > > > Here I have the pre-processed files after recon-all and a file called > > DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can run: > > > > dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o > > /usr/local/freesurfer/NPI001/DTI_15 > > > > Is this right? > > > > I will try by the time you answer but please let me know if you have > > any objection and/or advise. > > > > Many thanks, > > AK > > > > > > > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer > > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, August 31, 2011 1:49 PM > > *Subject:* Re: [Freesurfer]: Error with dt_recon > > > > If you pass it dicom, it will try to extract the bvalues, which is > > where it is failing. > > doug > > > > Antonella Kis wrote: > > > Dear Doug, > > > > > > Sorry but I still have a question about this error: > > > I understood that dt_recon it takes original dicom images as input > > and it generates multiple NIFTI volumes that will be used in later > > steps.So why I need to use the NIFTI as input? > > > > > > Thnak you. > > > AK > > > > > > > ------------------------------------------------------------------------ > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > *Cc:* "fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>" <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>; "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>" > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > *Sent:* Tuesday, August 30, 2011 3:51 PM > > > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > > > > > It's looking for the values in the dicom file (which apparently does > > not have them). Convert the dicom to nifit, then use the nifti as > > input, then pass files with bvals and bvects on the command line. > > > doug > > > > > > Antonella Kis wrote: > > > > > > > > > > > > Dear Bruce: > > > > > > > > I am running the dt_recon: > > > > # setenv FREESURFER_HOME /usr/local/freesurfer # setenv > > SUBJECTS_DIR $FREESURFER_HOME > > > > # cd /usr/local/freesurfer/NPI001 > > > > # dt_recon --i > > > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > > > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti > > > > > > > > > > > > and I am getting the following error: > > > > > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > > > > > Can you please give me a hint? > > > > > > > > Thank you. > > > > AK > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] : Error with dt_recon
by Douglas N Greve 31 Aug '11

31 Aug '11

That's almost right. Just specify the subject name and not the full path. Also, you will need to supply bvals and bvects dt_recon --i DTI_15.nii.gz --s NPI001 --o /usr/local/freesurfer/NPI001/DTI_15 Antonella Kis wrote: > Hi Doug, > > Thanks again for helping. So my question is then: I will pass for --i > (the input data) the .nii.gz file from the DTI data and the it is OK > to use for the --s which defines the file of the structural recon a > file called NPI001 where I have 10 files after recon-all (bem, label, > mri, surf, stats, etc)? In other words if I will set-up: > > setenv FREESURFER_HOME /usr/local/freesurfer > setenv SUBJECTS_DIR $FREESURFER_HOME > > and since my files are in /usr/local/freesurfer/NPI001 I am then doing: > > cd /usr/local/freesurfer/NPI001 > > Here I have the pre-processed files after recon-all and a file called > DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can run: > > dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o > /usr/local/freesurfer/NPI001/DTI_15 > > Is this right? > > I will try by the time you answer but please let me know if you have > any objection and/or advise. > > Many thanks, > AK > > > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, August 31, 2011 1:49 PM > *Subject:* Re: [Freesurfer]: Error with dt_recon > > If you pass it dicom, it will try to extract the bvalues, which is > where it is failing. > doug > > Antonella Kis wrote: > > Dear Doug, > > > > Sorry but I still have a question about this error: > > I understood that dt_recon it takes original dicom images as input > and it generates multiple NIFTI volumes that will be used in later > steps.So why I need to use the NIFTI as input? > > > > Thnak you. > > AK > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>> > > *Cc:* "fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>" <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>; "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Tuesday, August 30, 2011 3:51 PM > > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > > > It's looking for the values in the dicom file (which apparently does > not have them). Convert the dicom to nifit, then use the nifti as > input, then pass files with bvals and bvects on the command line. > > doug > > > > Antonella Kis wrote: > > > > > > > > > Dear Bruce: > > > > > > I am running the dt_recon: > > > # setenv FREESURFER_HOME /usr/local/freesurfer # setenv > SUBJECTS_DIR $FREESURFER_HOME > > > # cd /usr/local/freesurfer/NPI001 > > > # dt_recon --i > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti > > > > > > > > > and I am getting the following error: > > > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > > > Can you please give me a hint? > > > > > > Thank you. > > > AK > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] : Error with dt_recon
by Douglas N Greve 31 Aug '11

31 Aug '11

If you pass it dicom, it will try to extract the bvalues, which is where it is failing. doug Antonella Kis wrote: > Dear Doug, > > Sorry but I still have a question about this error: > I understood that dt_recon it takes original dicom images as input and > it generates multiple NIFTI volumes that will be used in later > steps.So why I need to use the NIFTI as input? > > Thnak you. > AK > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "fischl(a)nmr.mgh.harvard.edu" <fischl(a)nmr.mgh.harvard.edu>; > "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, August 30, 2011 3:51 PM > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > It's looking for the values in the dicom file (which apparently does > not have them). Convert the dicom to nifit, then use the nifti as > input, then pass files with bvals and bvects on the command line. > doug > > Antonella Kis wrote: > > > > > > Dear Bruce: > > > > I am running the dt_recon: > > # setenv FREESURFER_HOME /usr/local/freesurfer # setenv > SUBJECTS_DIR $FREESURFER_HOME > > # cd /usr/local/freesurfer/NPI001 > > # dt_recon --i > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti > > > > > > and I am getting the following error: > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > Can you please give me a hint? > > > > Thank you. > > AK > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Hippocampal subfilelds label
by Shashwath Meda 31 Aug '11

31 Aug '11

Hi Koen - I am looking at some hippocampal subfield measures on 3T and 7T and noticed that there is a label called "hippocampus" from your recent publications it was unclear what this label exactly meant? Is this a useful subfield measure to be considered for further analysis? What does this particular segment represent? Thanks, Shashwath Meda

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