[Freesurfer] -addtp option not working in recon-all -long
Hi all, I wanted to add a new timepoint in my longitudinal stream without recreating the base template. recon-all -help shows that I should be able to do that with: recon-all -long -addtp -all However, when I tried it I get an error. Here is the error: $recon-all -long miriad_189_AD_M_10SimulatedT1From01 miriad_189_AD_M_01_10 -addtp -all ERROR: miriad_189_AD_M_10SimulatedT1From01 is not in /home/bkhanal/works/freesurfer/freesurferSubjects/miriad_189_AD_M_01_10/base-tps Since I'm using a new timepoint which was not used in creating the base template it would of course not be in base-tps. Is -addtp no having any effect here ? The freesurfer version and my system info: Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Fedora release 19 (Schrödingerâs Cat) Kernel info: Linux 3.14.22-100.fc19.x86_64 x86_64 Thanks, Bishesh ___ 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] What exactly was wrong with DOSS in QDEC
Hello, I am dealing again with the "old" issue of using DOSS in QDEC. This option was removed. I cannot find any detailed explanations of what exactly was wrongly computed when selecting DOSS. I only find as explanation: "that there may be a bug in the way that QDEC computes contrasts for DOSS" "There is a bug in it that causes the contrasts to be in error at times" Which specific contrasts were actually affected? And how did it compute it instead of what? Did it happen all the time, or only sometimes, and why? Most important for me: Did it affect a group comparison using (nuisance) covariates? Or were the other additional correlation and interaction contrasts the ones which did not make sense? Would be nice to get some more insight into this. Thank you, Chris ___ 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] Desikan-Kilany atlas
Thanks for your reply Bruce, however I get an error when try to use this command. I'm in the directory containing the files and I ran *mri_surf2vol --surfval lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs --hemi lh --outvol LH.nii* and it gave me an output of *ERROR: cannot recognize the type of lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs* On Tue, Feb 24, 2015 at 4:42 PM, Bruce Fischl wrote: > I see. You could do what you want by sampling the ?h.aparc.annot into the > volume (mri_surf2vol), then mapping into MNI space (mri_vol2vol). Actually, > if you do surf2vol from fsaverage I think it's already in MNI coords, but > Doug can confirm. The problem is going to be that the mapping won't be very > accurate across subjects. You would be better off doing it all on the > surface > > cheers > > Bruce > > On Tue, 24 Feb 2015, Norman Benbrahim wrote: > > No problem, >> I want to take certain regions and use them as masks in order to compute >> the joint >> histogram between a thresholded z-score map obtained from ICA (a resting >> state >> network) masked in that region, and the variance of the BOLD image. I >> already have >> scripts set up to do this in matlab, so I would only need the atlas in >> nifti format >> so I can pick out which regions to use (using the rich club paper, van >> den Heuvel et >> al. 2011), and create masks out of those. >> >> On Tue, Feb 24, 2015 at 4:22 PM, Bruce Fischl >> wrote: >> Hi Norman >> >> perhaps you can take a step back and tell us what you want to use it >> for? >> We might be able to suggest a better analysis strategy >> Bruce >> On Tue, 24 Feb 2015, >> Norman Benbrahim wrote: >> >> > Hi, >> > I want to use the Desikan-Kilany atlas to run some analysis in >> some >> regions, however >> > I am very new to freesurfer. What I would like to accomplish is >> the >> following: >> > 1) Transform the atlas into MNI152 2mm space >> > 2) Convert the atlas to a binary nifti image (similarly to the way >> FSL's atlases are >> > stored) >> > If anyone can help me get started that would be awesome. Thank >> you! >> > -Norman >> > >> > >> ___ >> 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 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 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] Desikan-Kilany atlas
Hi Norman don't give it the gcs file as input - that's the atlas. Give it the lh.aparc.annot for that subject cheers Bruce On Wed, 25 Feb 2015, Norman Benbrahim wrote: Thanks for your reply Bruce, however I get an error when try to use this command. I'm in the directory containing the files and I ran mri_surf2vol --surfval lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs --hemi lh --outvol LH.nii and it gave me an output of ERROR: cannot recognize the type of lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs On Tue, Feb 24, 2015 at 4:42 PM, Bruce Fischl wrote: I see. You could do what you want by sampling the ?h.aparc.annot into the volume (mri_surf2vol), then mapping into MNI space (mri_vol2vol). Actually, if you do surf2vol from fsaverage I think it's already in MNI coords, but Doug can confirm. The problem is going to be that the mapping won't be very accurate across subjects. You would be better off doing it all on the surface cheers Bruce On Tue, 24 Feb 2015, Norman Benbrahim wrote: No problem, I want to take certain regions and use them as masks in order to compute the joint histogram between a thresholded z-score map obtained from ICA (a resting state network) masked in that region, and the variance of the BOLD image. I already have scripts set up to do this in matlab, so I would only need the atlas in nifti format so I can pick out which regions to use (using the rich club paper, van den Heuvel et al. 2011), and create masks out of those. On Tue, Feb 24, 2015 at 4:22 PM, Bruce Fischl wrote: Hi Norman perhaps you can take a step back and tell us what you want to use it for? We might be able to suggest a better analysis strategy Bruce On Tue, 24 Feb 2015, Norman Benbrahim wrote: > Hi, > I want to use the Desikan-Kilany atlas to run some analysis in some regions, however > I am very new to freesurfer. What I would like to accomplish is the following: > 1) Transform the atlas into MNI152 2mm space > 2) Convert the atlas to a binary nifti image (similarly to the way FSL's atlases are > stored) > If anyone can help me get started that would be awesome. Thank you! > -Norman > > ___ 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 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 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] Analyze format
Dear FS experts,I am trying to run recon-all on data with analyze format. I am aware that this is not the best format, however I do not have DICOM or NIFTI original data as this is a very old data from University of North Carolina. When I run import the images with recon-all -i. I am getting the following log below. Do you advice to proceed with recon-all -all or do you there is a way I could obtain the mat file that freesurfer is asking?Thank youPablorecon-all -i 30225.img -s 30225 mri_convert /home/0116442s/FS_test/30225.img /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz mri_convert /home/0116442s/FS_test/30225.img /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz -INFO: could not find /home/0116442s/FS_test/30225.mat file for direction cosine info.INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped.INFO: if not valid, please provide the information in /home/0116442s/FS_test/30225.mat file-$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /home/0116442s/FS_test/30225.img...TR=0.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, 0)j_ras = (0, 0, 1)k_ras = (0, 1, 0)writing to /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz... #-- recon-all -s 30225 finished without error at Wed Feb 25 15:30:09 GMT 2015done ___ 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] Analyze format
Hi Pablo the mat file is an extension to analyze the specifies the direction cosines. Without it we are only guessing at the anatomical orientation of the image. Unless these images have some marker such as a vitamin E capsule how will you ever know if we got left/right correct? cheers Bruce On Wed, 25 Feb 2015, pablo najt wrote: Dear FS experts,I am trying to run recon-all on data with analyze format. I am aware that this is not the best format, however I do not have DICOM or NIFTI original data as this is a very old data from University of North Carolina. When I run import the images with recon-all -i. I am getting the following log below. Do you advice to proceed with recon-all -all or do you there is a way I could obtain the mat file that freesurfer is asking? Thank you Pablo recon-all -i 30225.img -s 30225 mri_convert /home/0116442s/FS_test/30225.img /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz mri_convert /home/0116442s/FS_test/30225.img /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz - INFO: could not find /home/0116442s/FS_test/30225.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. INFO: if not valid, please provide the information in /home/0116442s/FS_test/30225.mat file - $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/0116442s/FS_test/30225.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, 1) k_ras = (0, 1, 0) writing to /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz... #-- recon-all -s 30225 finished without error at Wed Feb 25 15:30:09 GMT 2015 done ___ 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] A->P to P->A on GE 3T Discovery MR750
Hi Everyone, In order to introduce distortion correction methods in our DTI processing pipeline, I wanted to acquire B=0 with A->P to P->A phase encode directions, as recommended by topup tutorials. I talked to the MRI operators at our facility, and they were not able to find out how to flip the phase encoding directions on the GUI. We have GE 3T as mentioned on the subject line. Can someone let me know the way in which I can get these acquisitions on the GE scanner that we have? Currently, I would just like to have these filpped for the B=0, and not for the individual directions. Thanks, Sid ___ 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] long_mris_slopes error
Hi Carolina, probably you are not interested in the average thickness, so you can drop --do-avg . Also usually people decide between pc1 and spc. The stack is also not really necessary unless you want to look at it. Try to remove the trailing / at fsaverage and --sd $SUBJECTS_DIR that should fix your error. Best, Martin On 02/24/2015 01:54 PM, carolina.mr wrote: Hi FreeSurfer experts, I am trying to run Longitudinal Two Steps analysis. In the long_mris_slopes I run the following command: long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage/ --sd $SUBJECTS_DIR/ And, after some processing, it appears the error message: mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh mv: rename ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh to /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh: No such file or directory ERROR 1 : mv ./tmp-P01_TP_lh_thickness_C8c_pE/lh.tmp.mgh /analise//P01_TP/surf/lh.long.thickness-spc.fwhm0.fsaverage/.mgh did not work? In the base folder, /surf, I can find many .mgh archives, for example: lh.long.thickness-spc.fwhm0.mgh (and others with other fwhm smoothing factors). But I can't find any lh.long.thicknessfsaverage files. I did all the previous processing as it appears in the Longitudinal FS Tutorials. I also tried to run qcache with the base file, but it says it is not necessary, since it is a base file. Should I run qcache first with each subject / time point before? Thank you, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.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] -addtp option not working in recon-all -long
Hi Bishesh, that is weird, it should add the time point to that file. What version of FS are you using? Best, Martin On 02/25/2015 06:03 AM, Bishesh Khanal wrote: Hi all, I wanted to add a new timepoint in my longitudinal stream without recreating the base template. recon-all -help shows that I should be able to do that with: recon-all -long -addtp -all However, when I tried it I get an error. Here is the error: $recon-all -long miriad_189_AD_M_10SimulatedT1From01 miriad_189_AD_M_01_10 -addtp -all ERROR: miriad_189_AD_M_10SimulatedT1From01 is not in /home/bkhanal/works/freesurfer/freesurferSubjects/miriad_189_AD_M_01_10/base-tps Since I'm using a new timepoint which was not used in creating the base template it would of course not be in base-tps. Is -addtp no having any effect here ? The freesurfer version and my system info: Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Fedora release 19 (Schrödingerâs Cat) Kernel info: Linux 3.14.22-100.fc19.x86_64 x86_64 Thanks, Bishesh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.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] Any short route to parcellate only?
Hi folks, I am using the parcellation of Freesurfer for some other analyses. I see that the parcellation if obtained rather late in the pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all However, asking does not hurt: is there any short route to get the Desikan parcellation without doing the entire recon-all pipeline? I am not interested in thickness, template registration, etc. I need only the parcellation of gray matter in native space. Advice on other tools that can run parcellation quickly is also welcome. Dorian UPenn ___ 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] Any short route to parcellate only?
Hi Dorian, no, sorry, you pretty much need to run everything to get it. cheers Bruce On Wed, 25 Feb 2015, Dorian P. wrote: Hi folks, I am using the parcellation of Freesurfer for some other analyses. I see that the parcellation if obtained rather late in the pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all However, asking does not hurt: is there any short route to get the Desikan parcellation without doing the entire recon-all pipeline? I am not interested in thickness, template registration, etc. I need only the parcellation of gray matter in native space. Advice on other tools that can run parcellation quickly is also welcome. Dorian UPenn ___ 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] trac all -p
Hi Anastasia: I have run trac-all using the following command: trac-all -prep -c /data/alanf/FreeSurfer_5.3/diffusion_recons/dmrirc-101309 However, I get an error message which is as follows: INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3/diffusion_recons INFO: Diffusion root is /data/alanf/FreeSurfer_5.3/diffusion_recons/ Actual FREESURFER_HOME /cm/shared/freesurfer trac-preproc -c /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/scripts/dmrirc.local -log /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/scripts/trac-all.log -cmd /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/scripts/trac-all.cmd #- /cm/shared/freesurfer/bin/trac-preproc #- #@# Image corrections Wed Feb 25 11:52:55 EST 2015 mri_convert /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/dmri/dwi_orig.nii.gz mri_convert /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/dmri/dwi_orig.nii.gz niiRead(): error opening file /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz... crypt_gkey = *CbLO7a8FzSPM Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 25 11:52:55 EST 2015 Should I convert the nii.gz file to nii? I enclose the configuration file for your perusal. thank you so much, best, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Drug Abuse & Brain Imaging Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| dmrirc-101309 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] Convert between .m3z and .tm3d format outputs from mri_cvs_register
I using mri_cvs_register and applyMorph on a linux server ( freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I would like to be able to convert the output transform *.m3z to *.tm3d format, as using applyMorph with the .m3z file returns an error: After loading template extension = m3z terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) Is there an easy way to convert between these file formats? Thanks for your help. -zack -- *Zachary Greenberg* *Imaging Specialist* *Department of Neurological Surgery* *University of California, San Francisco* ___ 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 -p
Hi Alan - It can't find the file. Check the error message, part of the path to the file is repeated twice. I suspect you typed that part in both dcmroot and dcmlist. a.y On Wed, 25 Feb 2015, Alan Francis wrote: Hi Anastasia: I have run trac-all using the following command: trac-all -prep -c /data/alanf/FreeSurfer_5.3/diffusion_recons/dmrirc-101309 However, I get an error message which is as follows: INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3/diffusion_recons INFO: Diffusion root is /data/alanf/FreeSurfer_5.3/diffusion_recons/ Actual FREESURFER_HOME /cm/shared/freesurfer trac-preproc -c /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/scripts/dmrirc.local -log /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/scripts/trac-all.log -cmd /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/scripts/trac-all.cmd #- /cm/shared/freesurfer/bin/trac-preproc #- #@# Image corrections Wed Feb 25 11:52:55 EST 2015 mri_convert /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/dmri/dwi_orig.nii.gz mri_convert /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz /data/alanf/FreeSurfer_5.3/diffusion_recons//101309/dmri/dwi_orig.nii.gz niiRead(): error opening file /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data/alanf/FreeSurfer_5.3/diffusion_recons///data/alanf/FreeSurfer_5.3/diffusion_recons/101309/Diffusion/data.nii.gz... crypt_gkey = *CbLO7a8FzSPM Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 25 11:52:55 EST 2015 Should I convert the nii.gz file to nii? I enclose the configuration file for your perusal. thank you so much, best, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N. Francis PhD NIDA T32 Fellow in Drug Abuse & Brain Imaging Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu afran...@mclean.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] Convert between .m3z and .tm3d format outputs from mri_cvs_register
You can use createMorph: createMorph --out $tm3d --template $template \ --subject $moving --in gcam $m3z --Lilla On Wed, 25 Feb 2015, Zachary Greenberg wrote: I using mri_cvs_register and applyMorph on a linux server ( freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I would like to be able to convert the output transform *.m3z to *.tm3d format, as using applyMorph with the .m3z file returns an error: After loading template extension = m3z terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) Is there an easy way to convert between these file formats? Thanks for your help. -zack -- Zachary Greenberg Imaging Specialist Department of Neurological Surgery University of California, San Francisco ___ 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] -addtp option not working in recon-all -long
It's 5.3.0. Here is the freesurfer version and my system info: Build stamp: freesurfer-Linux-centos6_x86_ 64-stable-pub-v5.3.0 RedHat release: Fedora release 19 (Schrödinger’s Cat) Kernel info: Linux 3.14.22-100.fc19.x86_64 x86_64 On Wed, Feb 25, 2015 at 7:54 PM, Martin Reuter wrote: > Hi Bishesh, > > that is weird, it should add the time point to that file. What version of > FS are you using? > > Best, Martin > > > On 02/25/2015 06:03 AM, Bishesh Khanal wrote: > > Hi all, > I wanted to add a new timepoint in my longitudinal stream without > recreating the base template. recon-all -help shows that I should be able > to do that with: > recon-all -long -addtp -all > > However, when I tried it I get an error. > Here is the error: > $recon-all -long miriad_189_AD_M_10SimulatedT1From01 miriad_189_AD_M_01_10 > -addtp -all > ERROR: miriad_189_AD_M_10SimulatedT1From01 is not in > /home/bkhanal/works/freesurfer/freesurferSubjects/miriad_189_AD_M_01_10/base-tps > > Since I'm using a new timepoint which was not used in creating the base > template it would of course not be in base-tps. Is -addtp no having any > effect here ? > The freesurfer version and my system info: > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > RedHat release: Fedora release 19 (Schrödinger’s Cat) > Kernel info: Linux 3.14.22-100.fc19.x86_64 x86_64 > > Thanks, > Bishesh > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Dr. Martin Reuter > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.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 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] [FreeSurfer/TRACULA]
Hello, Where can we find the link to tract the inferior fronto-occipital fascicles? Just want to know the reference name to add it to my path list. Best, Walid ___ 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] warping segmentations onto unprocessed brain
Hi freesurfers, I am hoping to warp an aparc+aseg.mgh file from a subject's freesurfer-processed image to a separate (unprocessed) T1 image on the same subject. I would like to use a purely intensity-based nonlinear volumetric registration to do this, to save time and complication. I understand I can do this if I have a .m3z warp file. My question is, how can I get this warp file? I have tried using mri_cvs_register with the --step3 option, but that appears to only work after the surface-based registrations have been carried out. I haven't found another tool to do this yet. Are there any ideas? Thank you very much for your time. -David ___ 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] warping segmentations onto unprocessed brain
Is there any reason you need it to be nonlinear? I would think bbregister and mri_vol2vol would do the trick Cheers Bruce > On Feb 25, 2015, at 11:18 PM, David Grayson wrote: > > Hi freesurfers, > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to a separate (unprocessed) T1 image on the same > subject. I would like to use a purely intensity-based nonlinear volumetric > registration to do this, to save time and complication. I understand I can do > this if I have a .m3z warp file. > > My question is, how can I get this warp file? I have tried using > mri_cvs_register with the --step3 option, but that appears to only work after > the surface-based registrations have been carried out. I haven't found > another tool to do this yet. > > Are there any ideas? Thank you very much for your time. > > -David > ___ > 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] [FreeSurfer/TRACULA]
This tract is not included in our atlas. Please see the wiki for a list of available tracts. On Thu, 26 Feb 2015, Walid Yassin wrote: Hello, Where can we find the link to tract the inferior fronto-occipital fascicles? Just want to know the reference name to add it to my path list. Best, Walid ___ 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] warping segmentations onto unprocessed brain
Hey Bruce, Thanks for responding. I would actually prefer nonlinear. I did not mention it, but the aseg data that I have is on a distortion-corrected T1 image, whereas the unprocessed image I want to warp onto is the same scan but not corrected for distortion. The distortions are nonlinear. I was hoping there might be a way to get a warp field to go between the two images without running both images through the recon-all pipeline. Are there any other possible tools? Thanks! -David On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl wrote: > Is there any reason you need it to be nonlinear? I would think bbregister > and mri_vol2vol would do the trick > Cheers > Bruce > > > > > On Feb 25, 2015, at 11:18 PM, David Grayson > wrote: > > > > Hi freesurfers, > > > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to a separate (unprocessed) T1 image on the same > subject. I would like to use a purely intensity-based nonlinear volumetric > registration to do this, to save time and complication. I understand I can > do this if I have a .m3z warp file. > > > > My question is, how can I get this warp file? I have tried using > mri_cvs_register with the --step3 option, but that appears to only work > after the surface-based registrations have been carried out. I haven't > found another tool to do this yet. > > > > Are there any ideas? Thank you very much for your time. > > > > -David > > ___ > > 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 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.
