[Freesurfer] Longitudinal TRACULA - Error in path reconstruction
Hi Anastasia, I hope you’re enjoying your evening! I’m doing longitudinal TRACULA analysis on two subjects, each having two time points. I have already taken the steps of longitudinal recon-all and trac-all -prep & -bedp. Now I’m trying to do trac-all -path, but it gives me an error that I cannot recognize. I would greatly appreciate your help. I’ve attached the log files and the config file. Thank you so much, Emad Emad Ahmadi, MD --- Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu trc_.e11258806 Description: application/applefile trc_.o11258806 Description: Binary data trc_0001.e11258808 Description: application/applefile trc_0001.o11258808 Description: Binary data # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here #_ setenv SUBJECTS_DIR /cluster/guptagp/Emad/3LT/subjDir setenv RAW_DATA /cluster/guptagp/Emad/3LT/rawData #_ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # #set dtroot = /path/to/tracts/of/ducks # Subject IDs (one per time point per subject) #_ set subjlist = ( 2a \ 2b \ 3a \ 3b ) #_ # Longitudinal base template subject IDs (one for each time point above) #_ set baselist = ( 2tem \ 2tem \ 3tem \ 3tem ) #_ # In case you want to analyze only Huey and Louie # Default: Run analysis on all time points and subjects # #set runlist = (1 2 5 6) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) #_ set dcmroot = $RAW_DATA set dcmlist = ( 2a/Diffusion/IM-0001-0001.dcm \ 2b/Diffusion/IM-0001-0001.dcm \ 3a/Diffusion/IM-0001-0001.dcm \ 3b/Diffusion/IM-0003-0001.dcm ) #_ # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if inputs are not MGH DICOMs # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header #_ set bveclist = (/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \ /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \ /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \ /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt) #_ # Diffusion gradient table (if using the same one for all scans) # Must be specified if inputs are not MGH DICOMs # The table must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header #_ #set bvecfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt #_ # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header #_ set bvalfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bval.txt #_ # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # #set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # #set b0mlist = ( huey/year1/fmag/XXX-1.dcm \ huey/year2/fmag/XXX-1.dcm \ dewey/year1/fmag/XXX-1.dcm \ dewey/year2/fmag/XXX-1.dcm \ louie/year1/fmag/XXX-1.dcm \ louie/year2/fmag/XXX-1.dcm ) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # #set b0plist = ( huey/year1/fphas/XXX-1.dcm \ huey/year2/fphas/XXX-1.dcm \ dewey/year1/fphas/XXX-1.dcm \ dewey/year2/fphas/XXX-1.dcm \ louie/year1/fphas/XXX-1
[Freesurfer] Is the x-component of the b vectors extracted by mri_convert inverted?
Hi FreeSurfer Experts, Happy New Year! I am using mri_convert to extract b vectors (bvecs) from diffusion images obtained at Bay 4. Then I use TRACULA for reconstructing white-matter pathways. The shape of the reconstructed pathways are odd, so I checked if the extracted bvecs are correct. To check if the extracted bvecs are correct, I used Diffusion Toolkit together with the extracted bvecs to do deterministic tractography. Then I checked the shape of the extracted nerve fibers. I have put a slide deck in the following dropbox folder showing that the shape of the extracted nerve fibers don’t look right: https://www.dropbox.com/s/1bt6on0rwm9url6/x_inversion.pptx?dl=0 <https://www.dropbox.com/s/1bt6on0rwm9url6/x_inversion.pptx?dl=0> Then I inverted the x-components of the extracted bvecs, and did the tractography again. This corrected the shape of the extracted nerve fibers (see the slide deck). I additionally had a look at the extracted dtift_V1 vectors under the two conditions, i.e. before and after x-component inversion. The results showed the same thing: x inversion corrects the images. I just wanted to see if others have had the same problem and confirm that I should invert the x-component of the bvecs extracted via mri_convert (I had the same experience with dcm2nii tool, where I had to invert the z-component of the extracted bvecs). I hope a wonderful new year for everyone! Emad Emad Ahmadi, MD --- Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu <mailto:e...@nmr.mgh.harvard.edu>___ Freesurfer mailing list 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] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?
Hi Freesurfer experts, I hope you’re all enjoying your day! Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms obtained at Martinos Center. The dicoms have the following format: MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919 MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196 MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464 ... I receive error when I run dcm2niix (to extract the b values and b vectors): Command: dcm2niix -f dti The error I receive: Warning: output folder invalid MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try Error: unable to find any DICOM images in Conversion required 0.00 seconds. When I do the following steps to generate “treatable” dicoms, dcm2niix recognizes these dicoms: 1. copy Martinos Center dicoms to my local Mac 2. import dicoms into OsiriX 3. Export them as dicoms 4. copy the OsiriX-exported dicoms back to Launchpad 5. Run dcm2niix on the new dicoms Since this copying back and forth takes a lot of time, I need a better way to convert the “crazy” Martinos Center dicoms into the “treatable” ones! I would really appreciate your help. Best, Emad Emad Ahmadi, MD --- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list 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.
Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?
Hi, Thank you for your quick response! I have already copied the dicoms to my cluster space: /cluster/guptagp/Emad/Epilepsy/temp/slices and the permissions of this folder seem right to me: drwxrwsr-x 2 emad guptagp 32768 Oct 30 10:30 slices The permissions on the dicom files are the same: -bash-4.1$ ls -l MR1.3.12.2.1107.5.2.32.35006.2009021913370421213012700 -rwxrwxr-x 1 emad guptagp 2219694 Oct 30 10:30 MR1.3.12.2.1107.5.2.32.35006.2009021913370421213012700 Any thoughts? Best, Emad > On Oct 30, 2015, at 10:43 AM, dgw <dgwake...@gmail.com> wrote: > > Hi Emad, > > The only problems, which I have run into is major weaknesses in dcm2nii: > 1. You must have write permissions on the directory the files are > located in. > 2. dcm2nii cannot work on symbolically linked files. > > Therefore, first copy the files to your own analysis workspace: e.g. > /cluster// > then run dcm2nii. > With that I have no problems. > > hth > d > > On 10/30/15 10:28 AM, Emad Ahmadi wrote: >> Hi Freesurfer experts, >> >> I hope you’re all enjoying your day! >> >> Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms >> obtained at Martinos Center. The dicoms have the following format: >> >> MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919 >> MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196 >> MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464 >> ... >> >> I receive error when I run dcm2niix (to extract the b values and b >> vectors): >> >> Command: >> dcm2niix -f dti >> >> The error I receive: >> >> Warning: output folder invalid >> MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try >> Error: unable to find any DICOM images in >> Conversion required 0.00 seconds. >> >> When I do the following steps to generate “treatable” dicoms, dcm2niix >> recognizes these dicoms: >> >> 1. copy Martinos Center dicoms to my local Mac >> 2. import dicoms into OsiriX >> 3. Export them as dicoms >> 4. copy the OsiriX-exported dicoms back to Launchpad >> 5. Run dcm2niix on the new dicoms >> >> Since this copying back and forth takes a lot of time, I need a better >> way to convert the “crazy” Martinos Center dicoms into the “treatable” ones! >> >> I would really appreciate your help. >> >> Best, >> Emad >> >> >> Emad Ahmadi, MD >> --- >> Research Fellow >> Department of Radiology >> Massachusetts General Hospital >> Harvard Medical School >> >> 25 New Chardon Street, Suite 400 >> Boston, MA 02114 >> Tel: 617 726 5237 >> Email: e...@nmr.mgh.harvard.edu <mailto:e...@nmr.mgh.harvard.edu> >> <mailto:e...@nmr.mgh.harvard.edu <mailto:e...@nmr.mgh.harvard.edu>> ___ Freesurfer mailing list 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] Free surfer dev env doesn't extract bvals/bvecs
Hi Freesurfers,I’m using the dev env on Launchpad to analyze DTI dicoms using TRACULA.It cannot extract the bvecs from the dicom header since it gives me the following error:ERROR: Must specify input table of gradient vectorsI’ve attached the TRACULA configuration file (dmrirc3.txt) and the log file. I would appreciate your help!Best,Emad Emad Ahmadi, MD---Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email: e...@nmr.mgh.harvard.edu # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here #_ setenv SUBJECTS_DIR /cluster/guptagp/Emad/Epilepsy/subjDir setenv RAW_DATA /cluster/guptagp/Emad/Epilepsy/rawData #_ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # #set dtroot = /path/to/tracts/of/ducks # Subject IDs #_ set subjlist = (310) #_ # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # #set runlist = (1 3) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) #_ set dcmroot = $RAW_DATA set dcmlist = (310/DIFFUSION_high_res/slices/MR1.3.12.2.1107.5.2.32.35006.2009020220092419345382942) #_ # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if inputs are not MGH DICOMs # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # #set bveclist = () # Diffusion gradient table (if using the same one for all scans) # Must be specified if inputs are not MGH DICOMs # The table must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # #set bvecfile = /path/to/bvecs.txt # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # #set bvalfile = /path/to/bvals.txt # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # #set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # #set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # #set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # #set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # #set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # #set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # #set thrbet = 0.5 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 1 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 0 # Perform registration of T1 to MNI template? # Default: 1 (yes) # #set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # #set mnitemp = /path/to/mni_template.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # #set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # #set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # #set cvstempdir = /path/to/cvs/atlases/of/ducks # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # #set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # #set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP
[Freesurfer] Recon-all error
Hi,I keep getting an error when I run recon-all and can’t figure out what is wrong. I would really appreciate your help. I’ve attached the log file.Thank you so much,Emad Emad Ahmadi, MD---Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email:e...@nmr.mgh.harvard.edu recon-all.log Description: Binary data ___ Freesurfer mailing list 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.
Re: [Freesurfer] Trac-all error
Thank you so much, Zeke! That helped a lot. Best, Emad On Mar 10, 2015, at 11:43 PM, zkauf...@nmr.mgh.harvard.edu wrote: Hello Emad, The download page states that OSX versions of freesurfer require the user to download and install XQuartz onto their machine. I have updated the download page so it is a little more clear. https://surfer.nmr.mgh.harvard.edu/fswiki/Download https://surfer.nmr.mgh.harvard.edu/fswiki/Download Also, the dev version of freesurfer is in a high degree of flux right now. We are undergoing compiler upgrades and other various changes to the build. This means I would expect the nightly builds to be unstable for the next couple days. But installing XQuartz should resolve the issue you experienced below. -Zeke Hello Anastasia, Iâm using the nightly-built version for Mac OS Lion; I double checked it by the command freesurfer -ver and got this response: You are running this version of FreeSurfer: freesurfer-Darwin-lion-dev-20150227 Iâm using this version on Mac OS X Yosemite. I tried to re-download a nightly built version, but it didnât let me (presumably because itâs workshop time). Please let me know how I should proceed. Yours, Emad On Mar 6, 2015, at 7:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu wrote: Hi Emad - The error is: dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib Does the freesurfer build that you're using match the computer that you're running it on? a.y On Wed, 4 Mar 2015, Emad Ahmadi wrote: Hello Freesurfers! Iâm trying to use tracheal -prep, and Iâm getting an error. Would you please help me with figuring out where the problem is? The log file is attached. Thank you very much, Emad Emad Ahmadi, MD --- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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] TRACHEAL error
Hello Freesurfers!I’m trying to use tracheal -prep, and I’m getting an error. Would you please help me with figuring out where the problem is? The log file is attached.Thank you very much,EmadEmad Ahmadi, MD---Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email:e...@nmr.mgh.harvard.edu trac-all.log Description: Binary data ___ Freesurfer mailing list 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.
Re: [Freesurfer] TRACHEAL error
* I’m trying to use trac-all On Mar 4, 2015, at 4:42 PM, Emad Ahmadi e...@nmr.mgh.harvard.edu wrote: Hello Freesurfers! I’m trying to use tracheal -prep, and I’m getting an error. Would you please help me with figuring out where the problem is? The log file is attached. Thank you very much, Emad Emad Ahmadi, MD --- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu mailto:e...@nmr.mgh.harvard.edu trac-all.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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.
Re: [Freesurfer] Recon-all error
Thank you very much, Bruce! I ran it again and this time, it didn’t give me error. Yours, Emad On Jul 7, 2014, at 12:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: hmmm, hard to say. Is it possible that you ran out of memory? Maybe something else was running on the machine? Try rerunning and see if it is ok, and also monitor memory usage. It died right in the middle of mri_ca_label which I can't remember seeing before On Mon, 7 Jul 2014, Emad Ahmadi wrote: Hello FreeSurfers, Wish you a great summer time! I’m running recon-all on DICOM images of a healthy control, and it's giving me an error. I have attached the log file; I’m running FreeSurfer on a Mac computer and the version I’m using is: freesurfer-Darwin-lion-dev-20140701. I would really appreciate your help. Best, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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] Dura correction using MEMPRAGE vs bandwidth-matched FLAIR
Hi,We are at the start of a study on TBI, in which we’re obtaining MEMPRAGE and T2-SPACE-FLAIR images (the images are obtained in Lunder 6 scanner, and I wonder if I can find T1 FLAIR matched sequences for morphormetry on that scanner). The pixel size of the MEMPRAGE sequence is 1mm isotropic, while the one for T2-SPACE-FLAIR is 0.5 x 0.5 x 1mm; they’re not bandwidth matched either (I’ve attached the details of the sequences we’re using). I just wanted to know if we should make changes to our T2-SPACE-FLAIR sequence and match it with the MEMPRAGE sequence to feed the FLAIR images into recon-all for dura correction, or if we should leave the T2-SPACE-FLAIR sequence as it is and use the four echoes of MEMPRAGE for dura correction (I mean, is dura correction using different echoes of MEMPRAGE as good as feeding FLAIR images into recon-all?)Thank you very much,Emad Emad Ahmadi, MD---Postdoc Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email: e...@nmr.mgh.harvard.edu SIEMENS MAGNETOM Skyra syngo MR D13 - \\USER\RESEARCH\Gupta_Research\Main Sequences\MEMPRAGE_IPAT3 TA:4:28 PAT:3 Voxel size:1.0Ã1.0Ã1.0 mm Rel. SNR:1.00 :tfl_me - Properties Prio Recon Off Load to viewer On Inline movieOff Auto store images On Load to stamp segments Off Load images to graphic segments Off Auto open inline displayOff Wait for user to start On Start measurements single Routine Nr. of slab groups 1 Slabs 1 Dist. factor50 % PositionIsocenter Orientation Sagittal Phase enc. dir. A P AutoAlign --- Phase oversampling 0 % Slice oversampling 0.0 % FoV read256 mm FoV phase 100.0 % Slice thickness 1.00 mm TR 2530.0 ms TE 11.69 ms Averages1 Concatenations 1 Filter Prescan Normalize Coil elements HEA;HEP Contrast Magn. preparation Non-sel. IR TI 1100 ms Flip angle 7.0 deg Fat suppr. None Water suppr.None Averaging mode Long term Measurements1 Reconstruction Magn./Phase Multiple series Each measurement Resolution Base resolution 256 Phase resolution100 % Phase partial Fourier Off Interpolation Off PAT modeGRAPPA Accel. factor PE3 Ref. lines PE 32 Reference scan mode Integrated Image FilterOff Distortion Corr.Off Accel. factor 3D1 Unfiltered images Off Prescan Normalize On Normalize Off B1 filter Off Raw filter Off Elliptical filter Off Slice resolution100 % Slice partial Fourier Off Geometry Nr. of slab groups 1 Slabs 1 Dist. factor50 % PositionIsocenter Phase enc. dir. A P Phase oversampling 0 % Slice oversampling 0.0 % Slices per slab 176 Multi-slice modeSingle shot Series Interleaved Nr. of sat. regions 0 Position mode
[Freesurfer] Unpacking Problem
Hello,I’m trying to unpack and run recon-all on a set of MEMPRAGE images we’ve obtained in Lunder 6 scanner (Siemens Skyra), but recon-all is giving me errors. I’ve attached for the scan.info file (outputted by unpacksdcmdir), the unpack.config file that I used to unpack the MEMPRAGE images, and the recon-all.log file containing the error that recon-all command gives me. I’m running recon-all on in MEMPRAGE3 folder containing MEMPRAGE_IPAT3 RMS images. Please let me know if I have to provide any further info about this problem.Thank you very much for your help,EmadEmad Ahmadi, MD---Postdoc Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email: e...@nmr.mgh.harvard.edu scan.info Description: Binary data unpack.config Description: Binary data recon-all.log Description: Binary data ___ Freesurfer mailing list 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] Applying a precomputed transform matrix to an image in free surfer
Hello, I’m having a volume (e.g. dtifit_FA.nii.gz) and a transform matrix (e.g. diff2anatorig.bbr.mat), and I want to apply the transform matrix to the image and generate a transformed image. This is a general question I’m having, but in this particular case, I want to apply the transform matrix (from diffusion space to the anatomical space generated by TRACULA) to the FA map to generate a transformed FA map that can be overlaid on the anatomical images. I wonder if I have to use mri_vol2vol command for doing this, and I don’t know how to provide it with appropriate flags. I’m already having the transform matrix generated by TRACULA (and I don’t want to change it; I just want to apply it to the image!). My crude guess would be something like this: mri_vol2vol --mov address of dtifit_FA.nii.gz --o address of transformed_dtifit_FA.nii.gz --reg diff2anatorig.bbr.mat Please let me know how I should run this command. Thank you very much, Emad P.S. I know that for this particular example, I can use the anatomical images in dlabel/diff, but the point for me is to learn how to apply a transform matrix to an image and generate a transformed image in freesurfer Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu___ Freesurfer mailing list 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] How to define a new label for aparc+aseg.mgz in FreeView
Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list 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.
Re: [Freesurfer] How to define a new label for aparc+aseg.mgz in FreeView
Hi Bruce, Thank you for your response. I just want to draw manually the region of the new label on the images of few subjects. What I am about to do is to define a new label for the trigeminal nerve sensory nucleus (just roughly as the region that the nerve enters the brainstem); I just need to label it manually for all subjects. Best, Emad On Mar 3, 2014, at 11:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Emad do you mean draw one manually or add it so it is automatically labeled in new subjects? If the latter it requires manually labeling a training set and rebuilding a classifer, etc..., so it is far from trivial cheers Bruce On Mon, 3 Mar 2014, Emad Ahmadi wrote: Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list 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] How to clone from T1 to brainmask in freeview to amend a bad skull strip
Hi! I want to know how to clone from T1.mgz to brainmask.mgz in freeview (to amend a skullstript that has removed too much). I couldn’t find the tool in freeview. Thank you very much, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list 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] Recon-all error
Hello, I am using recon-all, and it gives me error and exits and I cannot understand why. I would appreciate it if you give me a clue why it's not working. I've written a piece of script (recon.bash attached) to be copied to the subject's folder, and when run it should automatically go through the analysis pipeline, but it gives me the error and exits. Thank you very much, Emad Emad Ahmadi, MD Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu recon-all.log Description: Binary data recon.bash Description: Binary data ___ Freesurfer mailing list 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] recon-all error
Hello Happy New Year! I'm running recon-all for one subject on MGH clusters (ERISone), and it exits with error. I would appreciate it if you help me figure out what the problem is. The log file is attached. All the best throughout 2014! Emad Emad Ahmadi, MD Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu recon-all.log Description: Binary data recon1job.bash Description: Binary data ___ Freesurfer mailing list 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] Recon-all exits with errors for a patient with TBI
Hello, I'm analyzing some images of patients with TBI. There's one of them having abnormalities in T1 images (skull fracture, epidural/intracranial hemorrhage, shifts) that can trouble image registration; when I run recon-all for this patient, it exits with errors. I wonder if it has anything to do with the abnormalities troubling the registration of T1 images. I've attached the log file, and some axial sections of the T1 images can be viewed here: https://drive.google.com/folderview?id=0B4AFmHFjy_bsbkotd2QyZjZ6dW8usp=sharing Thank you and Merry Christmas! Emad recon-all.log Description: Binary data ___ Freesurfer mailing list 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] Generating list of subjects: a tcsh scripting problem
Hello, I am having a tcsh scripting problem for generating a text file containing the list of subjects, and I would appreciate any help. I've explained my problem here: http://stackoverflow.com/q/20617206/2769441 All the best, Emad ___ Freesurfer mailing list 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] Do these bvec and bval files match?
Hello, I'm using TRACULA to analyze images obtained by a non-Siemens scanner, and I'm using dcm2niigui app to generate bvec and bval files from DICOMs. My question is whether or not the attached bvec and bval files match, because the 0 bval is the first entry while the 0,0,0 bvec is somewhere in the middle. If they don't, how should I generate the correct bval/bvec files from dicoms? Lots of thanks, Emad bval Description: Binary data bvec Description: Binary data ___ Freesurfer mailing list 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] Is there anyway to define multiple processing cores for FreeSurfer to speed up its commands?
Hello, I'm using FreeSurfer on a 6-core Mac Pro machine. It takes quite a bit for commands like recon-all to complete, while I've noticed that my CPU and memory resources are mostly idle. I just wanted to know if there's anyway to define multiple cores for FreeSurfer (something like matlabpool in matlab parallel computing toolbox). Thank you, Emad Emad Ahmadi, MD Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list 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.
