[Freesurfer] Tracula trac-all -prep error
External Email - Use Caution Hello, I am trying to run the command trac-all -prep -c dmrircmultiscan.example -jobs prep.txt using a config file made for a cross-sectional study with multiple scans. Each subjects has 2 scans. When I run the command I get this error message. length of pathway list (/proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt) and endpoint label ID list ERROR: () do not match Under the hood I noticed a gmids variable could be set. I this something I need to do for this data structure? I have previously not had issues using one scan. Below is the config file text. Thank you in advance! # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 or 2 # Default: 1 (yes) # set dorotbvecs = 1 # Intra-subject (diffusion-to-T1) registration method # 1: Affine with a correlation ratio cost # 2: Affine with a mutual information cost # 3: Affine with a boundary-based cost (default) # set intrareg = 3 # Degrees of freedom for intra-subject registration # Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine) # Default: 6 for infants, 9 otherwise # set intradof = 9 # Maximum rotation angle (degrees) for intra-subject registration # Default: 3 for infants, 90 otherwise # set intrarot = 90 # Inter-subject registration method # 1: Affine T1-to-T1 with a correlation ratio cost # 2: Affine T1-to-T1 with a mutual information cost # 3: Affine T1-to-T1 with a robust cost (default for infants) # 4: Nonlinear T1-to-T1 with CVS # 5: Nonlinear FA-to-FA with SyN (default) # set interreg = 5 # Target brain for inter-subject registration # Default for affine T1-to-T1: # $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Default for nonlinear T1-to-T1: # $FREESURFER_HOME/subjects/cvs_avg35/ # Default for nonlinear FA-to-FA: # $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # # I think this fixed my issue with syntax # set intertrg = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # Whole-brain segmentation used to extract the anatomical neighborhood priors # of the pathways of interest # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/$segname.mgz # Default: aparc+aseg # set segname = aparc+aseg # Use the thalamic nuclei segmentation? # This is highly recommended to use for any pathways that terminate in # or neighbor the thalamus # When used, it is merged with the whole-brain segmentation above # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz # Default: 1 (yes) # set usethalnuc = 0 # 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 # 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 # Paths to reconstruct # Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # set pathlist = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist (recommended, with more points for longer paths) # Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # set ncpts = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0 Jake R. Powell, MS, LAT, ATC Doctoral Student -
Re: [Freesurfer] surface/volume editing
External Email - Use Caution Hi again, Doug, I am just checking to make sure that the thread didn't get lost in the pile of requests, and whether or not you have had a chance to look at the surfaces I sent. Thanks Jake Jensen On Tue, Oct 6, 2020 at 10:08 AM Jake Jensen wrote: > Hi Doug, > > just following up to see if you had any suggestions for resolving the > problem of the ?h.wm surfaces not pulling back even after running it > through the pipeline. If you are in need of more screenshots or details, > let me know. > > Thanks, > > Jacob Jensen > > On Wed, Sep 30, 2020 at 8:37 AM Jake Jensen > wrote: > >> Here are some pictures of the pial (red), wm (yellow), and orig.nofix >> (green) surfaces with the brainmask.mgz and wm.mgz volumes >> >> >> >> On Wed, Sep 30, 2020 at 8:15 AM Douglas N. Greve >> wrote: >> >>> Can you send pictures of the ?h.orig.nofix surface in addition to the >>> white and pial? >>> >>> On 9/29/2020 12:24 PM, Jake Jensen wrote: >>> >>> External Email - Use Caution >>> Douglas, >>> >>> I have attempted to edit the wm.mgz and subsequently run -autorecon2. >>> However the ?h.white surface remains extended. >>> >>> I have attached some before and after editing pictures, which shows how >>> the wm surface does not recede even when it is removed. >>> >>> Thanks >>> >>> >>> >>> On Mon, Sep 28, 2020 at 9:04 AM Douglas N. Greve >>> wrote: >>> >>>> It looks like the orig extends too far, so try editing the wm.mgz >>>> >>>> On 9/25/2020 11:51 AM, Jake Jensen wrote: >>>> >>>> External Email - Use Caution >>>> Attached are a few snapshots of the ?.orig surfaces (pink), pial (red), >>>> and wm (yellow) >>>> >>>> On Fri, Sep 25, 2020 at 7:46 AM Douglas N. Greve < >>>> dgr...@mgh.harvard.edu> wrote: >>>> >>>>> Can you show it with the ?h.orig surfaces? Those should closely follow >>>>> the boundary of the wm.mgz volume >>>>> >>>>> On 9/23/2020 2:11 PM, Jake Jensen wrote: >>>>> >>>>> External Email - Use Caution >>>>> Hello, >>>>> >>>>> I am attempting to edit a subject, but upon removing voxels where the >>>>> WM and pial surfaces should not be, the WM surface does not >>>>> receed (pictures are attached). >>>>> >>>>> I have attempted this with -all and -autorecon2, running it again from >>>>> the original 001.mgz file, as well as attempting to run it from the >>>>> beginning with -clean. The end result is consistently the same, as seen in >>>>> the attached images. Additionally, it is strange that the WM surface >>>>> crosses the pial. >>>>> >>>>> I could not seem to find a solution to this in the archives. >>>>> >>>>> >>>>> FreeSurfer version: >>>>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >>>>> Platform: OSX mojave >>>>> -all -autorecon2 >>>>> >>>>> Recon all log attached >>>>> >>>>> Thank you! >>>>> >>>>> -Jacob >>>>> >>>>> >>>>> >>>>> ___ >>>>> Freesurfer mailing >>>>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >>>> >>>> >>>> ___ >>>> Freesurfer mailing >>>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >>> >>> >>> ___ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] surface/volume editing
External Email - Use Caution Hi Doug, just following up to see if you had any suggestions for resolving the problem of the ?h.wm surfaces not pulling back even after running it through the pipeline. If you are in need of more screenshots or details, let me know. Thanks, Jacob Jensen On Wed, Sep 30, 2020 at 8:37 AM Jake Jensen wrote: > Here are some pictures of the pial (red), wm (yellow), and orig.nofix > (green) surfaces with the brainmask.mgz and wm.mgz volumes > > > > On Wed, Sep 30, 2020 at 8:15 AM Douglas N. Greve > wrote: > >> Can you send pictures of the ?h.orig.nofix surface in addition to the >> white and pial? >> >> On 9/29/2020 12:24 PM, Jake Jensen wrote: >> >> External Email - Use Caution >> Douglas, >> >> I have attempted to edit the wm.mgz and subsequently run -autorecon2. >> However the ?h.white surface remains extended. >> >> I have attached some before and after editing pictures, which shows how >> the wm surface does not recede even when it is removed. >> >> Thanks >> >> >> >> On Mon, Sep 28, 2020 at 9:04 AM Douglas N. Greve >> wrote: >> >>> It looks like the orig extends too far, so try editing the wm.mgz >>> >>> On 9/25/2020 11:51 AM, Jake Jensen wrote: >>> >>> External Email - Use Caution >>> Attached are a few snapshots of the ?.orig surfaces (pink), pial (red), >>> and wm (yellow) >>> >>> On Fri, Sep 25, 2020 at 7:46 AM Douglas N. Greve >>> wrote: >>> >>>> Can you show it with the ?h.orig surfaces? Those should closely follow >>>> the boundary of the wm.mgz volume >>>> >>>> On 9/23/2020 2:11 PM, Jake Jensen wrote: >>>> >>>> External Email - Use Caution >>>> Hello, >>>> >>>> I am attempting to edit a subject, but upon removing voxels where the >>>> WM and pial surfaces should not be, the WM surface does not >>>> receed (pictures are attached). >>>> >>>> I have attempted this with -all and -autorecon2, running it again from >>>> the original 001.mgz file, as well as attempting to run it from the >>>> beginning with -clean. The end result is consistently the same, as seen in >>>> the attached images. Additionally, it is strange that the WM surface >>>> crosses the pial. >>>> >>>> I could not seem to find a solution to this in the archives. >>>> >>>> >>>> FreeSurfer version: >>>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >>>> Platform: OSX mojave >>>> -all -autorecon2 >>>> >>>> Recon all log attached >>>> >>>> Thank you! >>>> >>>> -Jacob >>>> >>>> >>>> >>>> ___ >>>> Freesurfer mailing >>>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >>> >>> >>> ___ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] surface/volume editing
External Email - Use Caution Attached are a few snapshots of the ?.orig surfaces (pink), pial (red), and wm (yellow) On Fri, Sep 25, 2020 at 7:46 AM Douglas N. Greve wrote: > Can you show it with the ?h.orig surfaces? Those should closely follow the > boundary of the wm.mgz volume > > On 9/23/2020 2:11 PM, Jake Jensen wrote: > > External Email - Use Caution > Hello, > > I am attempting to edit a subject, but upon removing voxels where the WM > and pial surfaces should not be, the WM surface does not receed (pictures > are attached). > > I have attempted this with -all and -autorecon2, running it again from the > original 001.mgz file, as well as attempting to run it from the beginning > with -clean. The end result is consistently the same, as seen in the > attached images. Additionally, it is strange that the WM surface crosses > the pial. > > I could not seem to find a solution to this in the archives. > > > FreeSurfer version: > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > Platform: OSX mojave > -all -autorecon2 > > Recon all log attached > > Thank you! > > -Jacob > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Edits to aparc+aseg
Hi FreeSurfers, I have a group of subjects with manual edits to the aparc+aseg volume. These edits were made to re-label unknown regions of cortex. I am wondering what recon-all flags I could use to implement the changes and re-generate cortical stats based on these edits. Thanks in advance. Best regards, Jake ___ 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] Unknown regions in cortical parcellation
We are using Freesurfer v6.0 Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve wrote: > what version of FS are you using? > > > On 09/07/2017 03:19 PM, Aidan Murphy wrote: > > > > We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the > > aparc volume we're noticing fairly large unknown regions in what > > should be entorhinal cortex, specifically where it comes up against > > the hippocampus and amygdala. The aseg volumes label these unknown > > regions as cortex. I've searched the archives and haven't been able to > > find anything similar from recent years. > > > > I've attached some axial screenshots of the raw T1, the aseg and the > > aparc+aseg. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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] Pial surface missing GM
Okay, understood. Thanks again for your help. Best regards, Jake On Fri, Jul 28, 2017 at 11:20 AM, Bruce Fischl wrote: > it depends. In this case you want to erase as it creates an incorrect > connection. In others you want to add if there is an incorrect break > On Fri, 28 Jul 2017, Jake Rieke wrote: > > Thanks, Bruce and Douglas! Looking at the surface prior to the topology >> correction step has been very helpful. I can see the region you pointed >> out >> - where the wm.mgz connects to the body of the wm, disconnects, and then >> reconnects at a different spot. I'm having some trouble implementing the >> manual edits to the wm.mgz. >> Part of the problem is that I'm still training my eye to differentiate GM >> and WM (especially in cases with thin tracts or partial voluming), but >> this >> gives me a great place to start. >> >> I'm wondering, in general, is the idea to erase or add voxels in the >> wm.mgz >> where the defects are located? In other words, defects can be interpreted >> as >> areas of misclassified as WM? In this case, it seems that I need to focus >> on >> deleting voxels in the wm.mgz that are incorrectly segmented. >> >> Thanks, >> Jake >> >> Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall >> VA >> Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 >> Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com >> >> On Thu, Jul 27, 2017 at 1:09 PM, Bruce Fischl > > >> wrote: >> Hi Jake >> >> there are voxels like 173, 112, 122 that are incorrectly >> segmented as wm (that is, they have a value >=5 in the wm.mgz) >> that connect two adjenct gyri. You can either change the >> intensity thresholds in mri_segment, or manually erase some of >> them. The best way to see this is to look at the surface prior >> to topology correction, and color it with defect numbers so you >> can see where the defects are. Something like: >> >> cd $SUBJECTS_DIR//mri >> freeview -v brain.mgz wm.mgz:colormap=heat:heatscale=1,100 \ >> -f../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels: >> overlay_threshold=1, >> 255:edgecolor=overlay \ >> -slice 172 123 134 >> >> >> if you page through a few axial slices you will see that the >> wm.mgz is connected to the body of the wm in slice 109, >> disconnecs in 110, then reconnects to a different part in 115, >> which should never happen >> >> cheers >> Bruce >>On Thu, 27 Jul 2017, Jake Rieke wrote: >> >> Hi Bruce, >> >> Thanks for the response. I just uploaded the subject >> using the ftp file >> exchange. The issue is visible in the region close >> to voxel coordinate [172, >> 123 ,134]. the missing gyrus is capped between >> coronal slice 141 to 118. I >> forgot to mention in my first message that we used a >> T2 to improve pial >> surface after initial running with just the T1. >> >> Thanks again >> Jake >> >> Biomedical Engineer, Brain Rehabilitation Research >> CenterMalcolm Randall VA >> Medical Center, 1601 SW Archer Road, Gainesville, FL >> 32608 >> Phone: 1-352-376-1611 ext. 5249, E-mail: >> jakeri...@gmail.com >> >> On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl >> >> wrote: >> Hi Jake >> >> usually that means that there is a topology >> defect that is being >> incorrectly fixed. If you upload the subject >> and point us at the >> voxel >> coords we will take a look >> >> cheers >> Bruce >> >> On Wed, 26 Jul 2017, Jake Rieke wrote: >> >> > Hello surfers, >> > >> > I'm attempting to extend white and pial >> surfaces to encompass >> an >> > unrecognized gyrus. The wm.mgz seems include >> the WM tiss
Re: [Freesurfer] Pial surface missing GM
Thanks, Bruce and Douglas! Looking at the surface prior to the topology correction step has been very helpful. I can see the region you pointed out - where the wm.mgz connects to the body of the wm, disconnects, and then reconnects at a different spot. I'm having some trouble implementing the manual edits to the wm.mgz. Part of the problem is that I'm still training my eye to differentiate GM and WM (especially in cases with thin tracts or partial voluming), but this gives me a great place to start. I'm wondering, in general, is the idea to erase or add voxels in the wm.mgz where the defects are located? In other words, defects can be interpreted as areas of misclassified as WM? In this case, it seems that I need to focus on deleting voxels in the wm.mgz that are incorrectly segmented. Thanks, Jake Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com On Thu, Jul 27, 2017 at 1:09 PM, Bruce Fischl wrote: > Hi Jake > > there are voxels like 173, 112, 122 that are incorrectly segmented as wm > (that is, they have a value >=5 in the wm.mgz) that connect two adjenct > gyri. You can either change the intensity thresholds in mri_segment, or > manually erase some of them. The best way to see this is to look at the > surface prior to topology correction, and color it with defect numbers so > you can see where the defects are. Something like: > > cd $SUBJECTS_DIR//mri > freeview -v brain.mgz wm.mgz:colormap=heat:heatscale=1,100 \ > -f ../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overl > ay_threshold=1,255:edgecolor=overlay \ > -slice 172 123 134 > > > if you page through a few axial slices you will see that the wm.mgz is > connected to the body of the wm in slice 109, disconnecs in 110, then > reconnects to a different part in 115, which should never happen > > cheers > Bruce > On Thu, 27 Jul 2017, Jake Rieke wrote: > > Hi Bruce, >> >> Thanks for the response. I just uploaded the subject using the ftp file >> exchange. The issue is visible in the region close to voxel coordinate >> [172, >> 123 ,134]. the missing gyrus is capped between coronal slice 141 to 118. I >> forgot to mention in my first message that we used a T2 to improve pial >> surface after initial running with just the T1. >> >> Thanks again >> Jake >> >> Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall >> VA >> >> Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 >> Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com >> >> On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl > > >> wrote: >> Hi Jake >> >> usually that means that there is a topology defect that is being >> incorrectly fixed. If you upload the subject and point us at the >> voxel >> coords we will take a look >> >> cheers >> Bruce >> >> On Wed, 26 Jul 2017, Jake Rieke wrote: >> >> > Hello surfers, >> > >> > I'm attempting to extend white and pial surfaces to encompass >> an >> > unrecognized gyrus. The wm.mgz seems include the WM tissue, >> but the white >> > surface does not extend to the WM boundary. I thought this >> might be related >> > to an intensity normalization error and tried using control >> points, but that >> > did not make a big difference in the resulting surfaces. I've >> attached >> > pictures to better illustrate the problem. Thanks in advance >> for your help! >> > >> > Best regards, >> > Jake >> > >> > >> > >> ___ >> 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] Pial surface missing GM
Hi Bruce, Thanks for the response. I just uploaded the subject using the ftp file exchange. The issue is visible in the region close to voxel coordinate [172, 123 ,134]. the missing gyrus is capped between coronal slice 141 to 118. I forgot to mention in my first message that we used a T2 to improve pial surface after initial running with just the T1. Thanks again Jake Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl wrote: > Hi Jake > > usually that means that there is a topology defect that is being > incorrectly fixed. If you upload the subject and point us at the voxel > coords we will take a look > > cheers > Bruce > > On Wed, 26 Jul 2017, Jake Rieke wrote: > > > Hello surfers, > > > > I'm attempting to extend white and pial surfaces to encompass an > > unrecognized gyrus. The wm.mgz seems include the WM tissue, but the white > > surface does not extend to the WM boundary. I thought this might be > related > > to an intensity normalization error and tried using control points, but > that > > did not make a big difference in the resulting surfaces. I've attached > > pictures to better illustrate the problem. Thanks in advance for your > help! > > > > Best regards, > > Jake > > > > > > > ___ > 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] average 4d volume
Hi! I tried to use mri_xvolavg to average a 4d nii volume, but does it need me to list each 3d volume separately? Is there a command that I can use to produce an average of a 4d volume, in one 3d image? Thanks in advance!! Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] is there a command to give resolution information?
Hi, This may be a frivolous question but I was just wondering if anyone knows a quick way to find out resolution of an image file, i.e., if I wanted to look at an older scan and wanted to check its resolution. I couldn't find any information in the wiki, but I may have just missed the correct area in my text search. Also, what if I wanted to confirm slice thickness? Thanks in advance! Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Registration file conversion
Hi Doug, I used the fslout command, but fsl is still looking for a header file when I try to use the matrix. [striatum:FSL_ASL_analysis] (nmr-std-env) applywarp --ref=swap_CTRL01_T1.nii.gz --in=swap_CTRL01_ASL.nii.gz --warp=CTRL01_fslreg.mat --out=swap_CTRL01_ASL_testwarp.nii.gz ** ERROR (nifti_image_read): failed to find header file for 'CTRL01_fslreg.mat' ** ERROR: nifti_image_open(CTRL01_fslreg.mat): bad header info Error: failed to open file CTRL01_fslreg.mat ERROR: Could not open image CTRL01_fslreg.mat Image Exception : #22 :: Failed to read volume CTRL01_fslreg.mat An error occured while reading file: CTRL01_fslreg.mat I feel like I'm missing something obvious.. thanks Jake > use tkregister2, something like > > tkregister2 --mov mov.nii --targ targ.nii --reg register.dat --fslout > fsl.mat --noedit > > and > > tkregister2 --mov mov.nii --targ targ.nii --reg register.dat --fsl > fsl.mat --noedit > > > John Kuster wrote: >> Dear Freesurfers, >> >> I was wondering if anyone can tell me if there is a command to convert >> an >> existing register.dat file from to .mat format for FSL, and vice versa. >> Thank you! >> >> Jake >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2 error
Hi, I am working on my workstation in the center. I don't currently have access to another machine as I am located in building 120. Is there something else I could try? thanks > Does that command work on other machines? Are you remotely logged in? > > j...@nmr.mgh.harvard.edu wrote: >> Hello, >> >> I am still getting the same error and can't figure out what mistake I >> may >> be making. Any help would be appreciated, >> >> thanks! >> Jake >> >> >> >> >> >> >>> Hi, I can't seem to open a window in tkregister2. Any help would be >>> appreciated, thanks! >>> >>> >>> [striatum:mri] (nmr-std-env) tkregister2 --targ orig.mgz --mov >>> /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr >>> --reg >>> /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/register.dat >>> tkregister_tcl /usr/local/freesurfer/stable4/lib/tcl/tkregister2.tcl >>> target volume orig.mgz >>> movable volume >>> /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr >>> reg file >>> /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/register.dat >>> LoadVol1 >>> ZeroCRAS 0 >>> $Id: tkregister2.c,v 1.86.2.9 2009/02/13 21:37:03 greve Exp $ >>> Diagnostic Level -1 >>> Input registration matrix >>> 1.004 0.010 -0.024 -0.800; >>> 0.122 -0.056 1.003 -1.403; >>> -0.009 0.998 0.056 6.038; >>> 0.000 0.000 0.000 1.000; >>> float2int = 2 >>> --- >>> INFO: loading target orig.mgz >>> INFO: changing target type to float >>> Ttarg: >>> -1.000 0.000 0.000 128.000; >>> 0.000 0.000 1.000 -128.000; >>> 0.000 -1.000 0.000 128.000; >>> 0.000 0.000 0.000 1.000; >>> INFO: loading movable >>> /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr >>> INFO: bvolumeRead: min = 0, max = 1508 >>> INFO: changing move type to float >>> Tmov: >>> -3.125 0.000 0.000 100.000; >>> 0.000 0.000 5.000 -75.000; >>> 0.000 -3.125 0.000 100.000; >>> 0.000 0.000 0.000 1.000; >>> mkheaderreg = 0, float2int = 2 >>> INFO: making tkreg matrix compatible with round >>> New registration matrix >>> 1.004 0.010 -0.023 0.769; >>> 0.123 -0.056 1.002 -3.866; >>> -0.008 0.998 0.056 4.482; >>> 0.000 -0.000 0.000 1.000; >>> --- >>> Input registration matrix >>> 1.004 0.010 -0.023 0.769; >>> 0.123 -0.056 1.002 -3.866; >>> -0.008 0.998 0.056 4.482; >>> 0.000 -0.000 0.000 1.000; >>> Determinant -1.01103 >>> subject = CD_R01BTX_ctrl2_sess2_recon >>> Zoom Factor = 2, SQR() = 4 >>> FOV = 256 >>> Opening window CD_R01BTX_ctrl2_sess2_recon >>> Can't create a context! >>> register: ### tkoInitWindow(name) failed >>> [striatum:mri] (nmr-std-env) >>> = >>> BUGR: >>> >>> FREESURFER_HOME: /usr/local/freesurfer/stable4 >>> >>> Build stamp: freesurfer-Linux-centos4-stable-v4.2.0e-20090311 >>> >>> RedHat release: CentOS release 5.2 (Final) >>> >>> Kernel info: Linux 2.6.18-92.1.22.el5 i686 >>> >>> NMR Center info (/space/freesurfer exists): >>> >>> machine: striatum >>> >>> SUBJECTS_DIR: /space/sake/3/users/inverse/subjects >>> >>> PWD: >>> /space/amaebi/35/users/ablood/R01_Botox/R01BTX_recons/CD_R01BTX_ctrl2_sess2_recon/mri >>> >>> >>> >>> ___ >>> 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 >> >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2 error
Hello, I am still getting the same error and can't figure out what mistake I may be making. Any help would be appreciated, thanks! Jake > Hi, I can't seem to open a window in tkregister2. Any help would be > appreciated, thanks! > > > [striatum:mri] (nmr-std-env) tkregister2 --targ orig.mgz --mov > /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr > --reg > /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/register.dat > tkregister_tcl /usr/local/freesurfer/stable4/lib/tcl/tkregister2.tcl > target volume orig.mgz > movable volume > /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr > reg file > /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/register.dat > LoadVol1 > ZeroCRAS 0 > $Id: tkregister2.c,v 1.86.2.9 2009/02/13 21:37:03 greve Exp $ > Diagnostic Level -1 > Input registration matrix > 1.004 0.010 -0.024 -0.800; > 0.122 -0.056 1.003 -1.403; > -0.009 0.998 0.056 6.038; > 0.000 0.000 0.000 1.000; > float2int = 2 > --- > INFO: loading target orig.mgz > INFO: changing target type to float > Ttarg: > -1.000 0.000 0.000 128.000; > 0.000 0.000 1.000 -128.000; > 0.000 -1.000 0.000 128.000; > 0.000 0.000 0.000 1.000; > INFO: loading movable > /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr > INFO: bvolumeRead: min = 0, max = 1508 > INFO: changing move type to float > Tmov: > -3.125 0.000 0.000 100.000; > 0.000 0.000 5.000 -75.000; > 0.000 -3.125 0.000 100.000; > 0.000 0.000 0.000 1.000; > mkheaderreg = 0, float2int = 2 > INFO: making tkreg matrix compatible with round > New registration matrix > 1.004 0.010 -0.023 0.769; > 0.123 -0.056 1.002 -3.866; > -0.008 0.998 0.056 4.482; > 0.000 -0.000 0.000 1.000; > --- > Input registration matrix > 1.004 0.010 -0.023 0.769; > 0.123 -0.056 1.002 -3.866; > -0.008 0.998 0.056 4.482; > 0.000 -0.000 0.000 1.000; > Determinant -1.01103 > subject = CD_R01BTX_ctrl2_sess2_recon > Zoom Factor = 2, SQR() = 4 > FOV = 256 > Opening window CD_R01BTX_ctrl2_sess2_recon > Can't create a context! > register: ### tkoInitWindow(name) failed > [striatum:mri] (nmr-std-env) > = > BUGR: > > FREESURFER_HOME: /usr/local/freesurfer/stable4 > > Build stamp: freesurfer-Linux-centos4-stable-v4.2.0e-20090311 > > RedHat release: CentOS release 5.2 (Final) > > Kernel info: Linux 2.6.18-92.1.22.el5 i686 > > NMR Center info (/space/freesurfer exists): > > machine: striatum > > SUBJECTS_DIR: /space/sake/3/users/inverse/subjects > > PWD: > /space/amaebi/35/users/ablood/R01_Botox/R01BTX_recons/CD_R01BTX_ctrl2_sess2_recon/mri > > > > ___ > 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
[Freesurfer] tkregister2 error
Hi, I can't seem to open a window in tkregister2. Any help would be appreciated, thanks! [striatum:mri] (nmr-std-env) tkregister2 --targ orig.mgz --mov /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr --reg /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/register.dat tkregister_tcl /usr/local/freesurfer/stable4/lib/tcl/tkregister2.tcl target volume orig.mgz movable volume /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr reg file /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/register.dat LoadVol1 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.9 2009/02/13 21:37:03 greve Exp $ Diagnostic Level -1 Input registration matrix 1.004 0.010 -0.024 -0.800; 0.122 -0.056 1.003 -1.403; -0.009 0.998 0.056 6.038; 0.000 0.000 0.000 1.000; float2int = 2 --- INFO: loading target orig.mgz INFO: changing target type to float Ttarg: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr INFO: bvolumeRead: min = 0, max = 1508 INFO: changing move type to float Tmov: -3.125 0.000 0.000 100.000; 0.000 0.000 5.000 -75.000; 0.000 -3.125 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 2 INFO: making tkreg matrix compatible with round New registration matrix 1.004 0.010 -0.023 0.769; 0.123 -0.056 1.002 -3.866; -0.008 0.998 0.056 4.482; 0.000 -0.000 0.000 1.000; --- Input registration matrix 1.004 0.010 -0.023 0.769; 0.123 -0.056 1.002 -3.866; -0.008 0.998 0.056 4.482; 0.000 -0.000 0.000 1.000; Determinant -1.01103 subject = CD_R01BTX_ctrl2_sess2_recon Zoom Factor = 2, SQR() = 4 FOV = 256 Opening window CD_R01BTX_ctrl2_sess2_recon Can't create a context! register: ### tkoInitWindow(name) failed [striatum:mri] (nmr-std-env) = BUGR: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.2.0e-20090311 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /space/amaebi/35/users/ablood/R01_Botox/R01BTX_recons/CD_R01BTX_ctrl2_sess2_recon/mri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon surf folder is missing data
Thank you Bruce and Doug > but remember to delete the IsRunning file > > Bruce Fischl wrote: >> Hi Jake >> >> looks like recon-all stopped in the middle of running. You can see >> this because (1) the recon-all.log file is in the middle of the >> surface deformation, with no error message or termination notice, and >> (2) there is an IsRunning.lh+rh in the scripts dir, meaning FreeSurfer >> thinks the recon is currently running. You can finish it with: >> >> recon-all -s $subject -sd $SUBJECTS_DIR -make all >> >> cheers, >> Bruce >> >> >> On Tue, 10 Mar 2009 j...@nmr.mgh.harvard.edu wrote: >> >>> Hi All, >>> >>> I was just wondering if anyone has had data missing from the surf >>> directory in the recon folder of a subject, ie- right hemisphere data >>> is >>> missing, or no data at all. Here is the path to a recon where I >>> recently have found missing data: >>> >>> /space/amaebi/35/users/ablood/R01_Botox/R01BTX_recons/CD_R01BTX_pat2_sess4_recon_missing_surfdata >>> >>> >>> Any help would be greatly appreciated, >>> >>> thanks >>> Jake >>> ___ >>> 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 >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon surf folder is missing data
Hi All, I was just wondering if anyone has had data missing from the surf directory in the recon folder of a subject, ie- right hemisphere data is missing, or no data at all. Here is the path to a recon where I recently have found missing data: /space/amaebi/35/users/ablood/R01_Botox/R01BTX_recons/CD_R01BTX_pat2_sess4_recon_missing_surfdata Any help would be greatly appreciated, thanks Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] preprocessing error
Hi, I am attempting to run the following command: preproc-sess -s CD_R01BTX_ctrl1_sess1 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 and am getting an error: >>>Tue Jan 27 16:33:44 EST 2009 >>>mcparams2exterg: finished >>>\n\n >>>Tue Jan 27 16:33:44 EST 2009 >>>mc-sess completed SUCCESSFULLY >>>CD_R01BTX_ctrl1_sess1 Smooth >>>Tue Jan 27 16:33:44 EST 2009 >>>/autofs/space/amaebi_035/users/ablood/R01_Botox >>>spatialsmooth-sess -i fmc5 -o fmcsm5 -fwhm 5 -fsd bold -umask 2 -s >>>CD_R01BTX_ctrl1_sess1 -d /autofs/space/amaebi_035/users/ablood/R01_Botox >>> >>> >>> >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1 >>>Tue Jan 27 16:33:45 EST 2009 >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1/bold >>>/space/amaebi/35/users/ablood/R01_Botox >>>RunList 016 017 018 019 020 021 >>>-- >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1/bold >>>ipfsl -i 016/fmc5 -o 016/fmcsm5 -pct .1 -fwhm 5 -fmt bhdr >>>-- >>>ERROR: cannot find /usr/pubsw/packages/fsl/4.1.2/bin/ip >>>ERROR: ipfsl failed >>>ERROR: spatialsmooth-sess failed Can anyone tell me what I am doing wrong? thanks!! Jake Bugr FREESURFER_HOME: /usr/local/freesurfer/stable3 >>>we have to use stable3 for specific reasons Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/amaebi/35/users/ablood/R01_Botox PWD: /space/amaebi/35/users/ablood/R01_Botox ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] stable3
Hello! I was just wondering if there is anything going on with the stable3 environment, or any changes currently being tweaked. The reason is that I have a script for analysis that sometimes says "ispl failed" which usually resolves itself if I wait a day or two, but hasnt resolved as of yet. Thanks, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] diffusion unpacksdcmdir error-wrong run!
Hi, Running the following command line : unpacksdcmdir -src /media/AJB_CERV1A/07311357 -targ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015 dti NII ajb_cerv_1a_dti.nii -unpackerr I encountered an error of the wrong run being unpacked. Instead of 15 as designated, 13 appears to have unpacked. This is data from our CD backup. This does not seems to be related to environment, because I originally tried to unpack in STD environment with same results, though all the original analysis was done in stable3 in 2004 when the scans were collected. The logfile is following after bugr. Thanks in advance! Jake BUGR: FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti Log file created by unpacksdcmdir $Id: unpacksdcmdir,v 1.12 2006/01/24 18:04:33 greve Exp $ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/unpack.log /autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti Mon Nov 3 14:19:09 EST 2008 -src /media/AJB_CERV1A/07311357 -targ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015 dti NII ajb_cerv_1a_dti.nii -unpackerr dicomdir /media/AJB_CERV1A/07311357 Scanning source directory ... INFO: summary file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile INFO: status file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status INFO: scanning path to Siemens DICOM DIR: /media/AJB_CERV1A/07311357 INFO: Found 1758 files in /media/AJB_CERV1A/07311357 INFO: counting Siemens Files $Id: mri_parse_sdcmdir.c,v 1.13.2.1 2006/05/15 21:42:35 greve Exp $ cwd /autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti cmdline --sortbyrun --d /media/AJB_CERV1A/07311357 --o /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile --status /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status sysname Linux hostname striatum machine i686 user jake INFO: found 1756 Siemens Files INFO: scanning info from Siemens Files INFO: status file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 INFO: found 1756 Siemens files syngo MR 2004A 4VA25A Sorting Assigning Run Numbers RunNo = 0 RunNo = 1 RunNo = 2 RunNo = 3 RunNo = 4 RunNo = 5 RunNo = 6 RunNo = 7 RunNo = 8 RunNo = 9 RunNo = 10 RunNo = 11 RunNo = 12 RunNo = 13 RunNo = 14 WARNING: Run 11 appears to be truncated Files Found: 78, Files Expected (lRep+1): 126 FileName/media/AJB_CERV1A/07311357/58851927 Identification NumarisVersyngo MR 2004A 4VA25A ScannerModel Allegra PatientName ajb_cerv_1a Date and time StudyDate 20040731 StudyTime 121222.984000 SeriesTime130908.562000 AcqTime 130848.812487 Acquisition parameters PulseSeq epfid2d1_64 Protocol ge_functionals PhEncDir COL EchoNo0 FlipAngle 90 EchoTime 30 InversionTime 30 RepetitionTime2500 PhEncFOV 200 ReadoutFOV200 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows384 NImageCols384 NFrames 78 SliceArraylSize 30 IsMosaic 1 ImgPos581.7606 607.9159 80.1682 VolRes 3.1250 3.1250 5. VolDim 64 64 30 Vc -0.9896 -0.0181 -0.1426 Vr 0.0368 -0.9909 -0.1294 Vs -0.1389 -0.1333 0.9813 VolCenter 0. 0. 0. TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: Run 15 appears to be truncated Files Found: 70, Files Expected (lRep+1): 1 FileName/media/AJB_CERV1A/07311357/58844259 Identification NumarisVersyngo MR 2004A 4VA25A ScannerModel Allegra PatientName ajb_cerv_1a Date and time StudyDate 20040731 StudyTime 121222.984000 SeriesTime134037.953000 AcqTime 134005.220012 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL
[Freesurfer] unpacking from CD backup
Hi, Could someone please explain how to unpack an old session saved on a CD? What command line should be used? thank you in advance, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Old scanning sessions, are they gone?
Hi! I am trying to unpack an old scannning session from 2004. In the standard env using findsession, it displays the following: [striatum:OLD_cerv_data] (nmr-std-env) findsession cerv_botox_ctrl1 === SUBJECT: cerv_botox_ctrl1 SUBJ ID: cerv_botox_ctrl1 DATE : October 26, 2004 TIME : 13:48:27 XPRMNTR: PATH : /space/archive/29/siemens/Allegra-20401-20041026-134339-796000 However, upon attempting to unpack, the error occurs: ERROR: directory /space/archive/29/siemens/Allegra-20401-20041026-134339-796000 does not exist. I have other old sessions that have shown the same results. Are the data actually there? Thanks in advance for you help, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkregister2
Hello, I am running the following command in the standard environment: tkregister2 --targ orig.mgz --mov /space/amaebi/35/users/ablood/DMRF_ASL/CD_DMRFASL_pat3_sess1/bold/021/fmcsm4.bhdr --reg /space/amaebi/35/users/ablood/DMRF_ASL/CD_DMRFASL_pat3_sess1/bold/register.dat this command has shown that the registration (created from autoreg-sess) has warped the functional data. I would like to run tkregister2 without the register.dat file, so I can use the orignal unwarped data. Is there a simple way to do so? Thanks in advance , Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon with only 1 mprage?
Hi! Can anyone tell me what possible issues there are with only using one mprage in creating a recon? [Our first mprage is crashing the reconstruction, and we have found that there was an error of some sort during that mprage, thus the need to do the recon with only the second mprage.] Thanks in advance, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ipfsl failed
Hello, I received the following error: (csh executable, ran from /autofs/homes/014/jake/AnalysisPrograms/CD_DMRFASL_ctrl2_ContrastAnalysis.csh) /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2 Mon May 19 10:16:02 EDT 2008 /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2/bold /space/amaebi/35/users/ablood/DMRF_ASL RunList 019 020 021 022 023 024 -- /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2/bold ipfsl -i 019/fmc4 -o 019/fmcsm4 -pct .1 -fwhm 4 -fmt bhdr -- ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed bugr: REESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects (looking at logfile, for the command dir is /space/amaebi/35/users/ablood/DMRF_ASL.) PWD: /space/amaebi/35/users/ablood/DMRF_ASL/log (logfile in log directory is preproc-CD_DMRFASL_ctrl2-bold.log) If anyone can help me, (im new to this) I would greatly appreciate it. Thank you in advance, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] unpacksdcmdir issue
Hello, I am getting an error saying that the path from the findsession command is not found. Here is the bugr information and following is the log from my terminal window; could anyone explain why the directory from findsession is missing? THANKS! FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.0.4-20080508 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/amaebi/35/users/ablood/R01_Botox PWD: /space/amaebi/35/users/ablood/R01_Botox striatum:jake[81] cd /space/amaebi/35/users/ablood/R01_Botox striatum:jake[82] source /usr/local/freesurfer/nmr-std-env freesurfer-Linux-centos4-stable-v4.0.4-20080508 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable4 FSFAST_HOME /usr/local/freesurfer/stable4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable4/mni FSL_DIR /usr/pubsw/packages/fsl/current [striatum:R01_Botox] (nmr-std-env) setenv SUBJECTS_DIR /space/amaebi/35/users/ablood/R01_Botox [striatum:R01_Botox] (nmr-std-env) findsession CD_RO1BTX_pat1_sess1 === SUBJECT: CD_RO1BTX_pat1_sess1 SUBJ ID: CD_RO1BTX_pat1_sess1 DATE : May 03, 2008 TIME : 19:27:12 XPRMNTR: PATH : /space/archive/160/siemens/TrioTim-35162-20080503-192630-556000 [striatum:R01_Botox] (nmr-std-env) unpacksdcmdir -src /space/archive/160/siemens/TrioTim-35162-20080503-192630-556000 -targ /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_pat1_sess1 -scanonly CD_RO1BTX_pat1_sess1_info $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $ /autofs/space/amaebi_035/users/ablood/R01_Botox -src /space/archive/160/siemens/TrioTim-35162-20080503-192630-556000 -targ /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_pat1_sess1 -scanonly CD_RO1BTX_pat1_sess1_info Fri May 9 10:51:51 EDT 2008 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2008/05/09-14:51:51-GMT BuildTimeStamp: May 8 2008 03:44:12 CVS: $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ User: jake Machine: striatum Platform: Linux PlatformVersion: 2.6.18-8.1.15.el5 CompilerName: GCC CompilerVersion: 30400 striatum Linux striatum 2.6.18-8.1.15.el5 #1 SMP Mon Oct 22 08:32:04 EDT 2007 i686 i686 i386 GNU/Linux ERROR: directory /space/archive/160/siemens/TrioTim-35162-20080503-192630-556000 does not exist [striatum:R01_Botox] (nmr-std-env) cd /space/archive/160/siemens/ /space/archive/160/siemens/: No such file or directory. [striatum:R01_Botox] (nmr-std-env) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Fwd: Re: [Freesurfer] Error]
I apologize, the csh file is located in the home directory, /homes/14/jake/AnalysisPrograms Thanks > Hi, > > Thanks for the bugr command. Here is my information, Thank you! > > > Please include the following additional information in your report: > > 1) subject name: > > CD_aftbotox_ctrl5 > > 2) the entire command-line executed > > csh CD_aftbotox_ctrl5_ContrastAnalysis.csh > > 3) the error message generated (please see below, our preprocessing > step is built into our csh file.) > > 4) optionally include the subject's /script/recon-all.log > **The logfile for preprocessing can be found in: >> /autofs/space/meso_018/users/ablood/cerv/log >> striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log > > > - > > FREESURFER_HOME: /usr/local/freesurfer/stable3 > > Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 > > RedHat release: CentOS release 5 (Final) > > Kernel info: Linux 2.6.18-8.1.15.el5 i686 > > NMR Center info (/space/freesurfer exists): > > machine: striatum > > SUBJECTS_DIR: /space/sake/3/users/inverse/subjects > > ***(this is set to be /space/meso/18/users/ablood/cerv by the .csh script) > > PWD: /homes/14/jake/AnalysisPrograms > > - > > > > > > > Original Message > Subject: Re: [Freesurfer] Error > From:"Pratap Kunwar" <[EMAIL PROTECTED]> > Date:Fri, March 28, 2008 12:00 pm > To: [EMAIL PROTECTED] > -- > > Jake, > > Are you doing preprocessing or stxgrinder, and are you running from >> *running from the following directory >> /autofs/homes/014/jake/AnalysisPrograms > > or > /autofs/space/meso_018/users/ablood/cerv/ ? > > it will be nice if you provide more info. use "bugr" to get report and > send to freesurfer. > about bugreporting, > https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?action=highlight&value=bugr > > pratap > >> Hi, >> >> We are getting an error where our preprocessing step seems to be >> failing, >> any help would be greatly appreciated, thank you! >> >> > >> >> *using the following command (which sources >> /usr/local/freesurfer/nmr-stable3-env) >> striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh >> >> *error: >> --- Parsing Config File: >> /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg >> >> -gammafit 2.25 1.25 -timewindow 25. -prestim 0 -polyfit 1 -TER >> 2.5000 >> -nskip 0 -fwhm 0 -rescale 1000 >> ERROR: 022/fmcsm4 does not have a .meanval file, run inorm >> ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): >> selxavg failed >> ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat >> -- >> stxgrinder-sess logfile is >> /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log >> -- >> ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for >> /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 >> >> >> >> >> >> >> >> **The logfile for preprocessing can be found in: >> /autofs/space/meso_018/users/ablood/cerv/log >> striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log >> >> ***Here is the error from the logfile: >> to3d WARNING: >> Significant outliers detected in these sub-bricks: >> 60 103 104 105 106 107 108 120 122 >> You should inspect the dataset for possible corruption. >> [Outliers are defined as in program 3dToutcount. ] >> [Outliers early in an EPI time series may be due to ] >> [the longitudinal magnetization equilibration effect.] >> [Other causes are subject movement, scanner problems,] >> [or anything that makes a time series look irregular.] >> [ 3dToutcount -save outnam dataset | 1dplot -stdin ] >> [can be used to make a dataset 'outnam' that marks ] >> [outlier voxels; see 3dToutcount -help for details. ] >> >> ++ 3D dataset written to disk >> -- Motion Correcting --- >> /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp >> set VR = 3dvolreg >> 3dvolreg -verbose -dfile >> /autofs/space/meso_
[Fwd: Re: [Freesurfer] Error]
Hi, Thanks for the bugr command. Here is my information, Thank you! Please include the following additional information in your report: 1) subject name: CD_aftbotox_ctrl5 2) the entire command-line executed csh CD_aftbotox_ctrl5_ContrastAnalysis.csh 3) the error message generated (please see below, our preprocessing step is built into our csh file.) 4) optionally include the subject's /script/recon-all.log **The logfile for preprocessing can be found in: > /autofs/space/meso_018/users/ablood/cerv/log > striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log - FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects ***(this is set to be /space/meso/18/users/ablood/cerv by the .csh script) PWD: /homes/14/jake/AnalysisPrograms - Original Message Subject: Re: [Freesurfer] Error From:"Pratap Kunwar" <[EMAIL PROTECTED]> Date:Fri, March 28, 2008 12:00 pm To: [EMAIL PROTECTED] -- Jake, Are you doing preprocessing or stxgrinder, and are you running from > *running from the following directory > /autofs/homes/014/jake/AnalysisPrograms or /autofs/space/meso_018/users/ablood/cerv/ ? it will be nice if you provide more info. use "bugr" to get report and send to freesurfer. about bugreporting, https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?action=highlight&value=bugr pratap > Hi, > > We are getting an error where our preprocessing step seems to be failing, > any help would be greatly appreciated, thank you! > > > > *using the following command (which sources > /usr/local/freesurfer/nmr-stable3-env) > striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh > > *error: > --- Parsing Config File: > /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg > > -gammafit 2.25 1.25 -timewindow 25. -prestim 0 -polyfit 1 -TER 2.5000 > -nskip 0 -fwhm 0 -rescale 1000 > ERROR: 022/fmcsm4 does not have a .meanval file, run inorm > ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): > selxavg failed > ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat > -- > stxgrinder-sess logfile is > /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log > -- > ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 > > > > > > > > **The logfile for preprocessing can be found in: > /autofs/space/meso_018/users/ablood/cerv/log > striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log > > ***Here is the error from the logfile: > to3d WARNING: > Significant outliers detected in these sub-bricks: > 60 103 104 105 106 107 108 120 122 > You should inspect the dataset for possible corruption. > [Outliers are defined as in program 3dToutcount. ] > [Outliers early in an EPI time series may be due to ] > [the longitudinal magnetization equilibration effect.] > [Other causes are subject movement, scanner problems,] > [or anything that makes a time series look irregular.] > [ 3dToutcount -save outnam dataset | 1dplot -stdin ] > [can be used to make a dataset 'outnam' that marks ] > [outlier voxels; see 3dToutcount -help for details. ] > > ++ 3D dataset written to disk > -- Motion Correcting --- > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp > set VR = 3dvolreg > 3dvolreg -verbose -dfile > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct > rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] > 6776+orig > ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] > ++ Authored by: RW Cox > ++ Reading in base dataset ./targ-6776+orig.BRIK > ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same > dimensi > ons! >Input: nx=64 ny=64 nz=30 >Base: nx=64 ny=64 nz=16 > ** FATAL ERROR: perhaps you could make your datasets match? > set st = 1 > if ( 1 ) then > echo ERROR: 3dvolreg existed with status 1 > ERROR: 3dvolreg existed with status 1 > exit 1 > ERROR: mc-sess failed > &g
[Freesurfer] Error
Hi, We are getting an error where our preprocessing step seems to be failing, any help would be greatly appreciated, thank you! *running from the following directory /autofs/homes/014/jake/AnalysisPrograms *using the following command (which sources /usr/local/freesurfer/nmr-stable3-env) striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh *error: --- Parsing Config File: /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg -gammafit 2.25 1.25 -timewindow 25. -prestim 0 -polyfit 1 -TER 2.5000 -nskip 0 -fwhm 0 -rescale 1000 ERROR: 022/fmcsm4 does not have a .meanval file, run inorm ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): selxavg failed ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat -- stxgrinder-sess logfile is /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log -- ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 **The logfile for preprocessing can be found in: /autofs/space/meso_018/users/ablood/cerv/log striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log ***Here is the error from the logfile: to3d WARNING: Significant outliers detected in these sub-bricks: 60 103 104 105 106 107 108 120 122 You should inspect the dataset for possible corruption. [Outliers are defined as in program 3dToutcount. ] [Outliers early in an EPI time series may be due to ] [the longitudinal magnetization equilibration effect.] [Other causes are subject movement, scanner problems,] [or anything that makes a time series look irregular.] [ 3dToutcount -save outnam dataset | 1dplot -stdin ] [can be used to make a dataset 'outnam' that marks ] [outlier voxels; see 3dToutcount -help for details. ] ++ 3D dataset written to disk -- Motion Correcting --- /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp set VR = 3dvolreg 3dvolreg -verbose -dfile /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] 6776+orig ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] ++ Authored by: RW Cox ++ Reading in base dataset ./targ-6776+orig.BRIK ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same dimensi ons! Input: nx=64 ny=64 nz=30 Base: nx=64 ny=64 nz=16 ** FATAL ERROR: perhaps you could make your datasets match? set st = 1 if ( 1 ) then echo ERROR: 3dvolreg existed with status 1 ERROR: 3dvolreg existed with status 1 exit 1 ERROR: mc-sess failed Thanks, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Copying control points file?
If I have the same subject on 2 different computers, but I edited the control points on one, can I just copy the tmp/control.dat file over to the other computer and rerun autorecon2-cp, or are there other files it refrences? Thanks-- -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Bad File Descriptor?
I am guessing that this is a general file error, not something specifically related to freesurfer, but was wondering if anyone had an idea on what might be wrong. 18 vertices at 20 distance writing curvature file /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/surf/lh.thickness tee: /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/scripts/recon-all.log: Bad file descriptor Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Tue Aug 8 07:03:55 PDT 2006 Thanks -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recon all finished with errors, How do I see what errors?
I was running autorecon2-cp and it said it finished with errors, below are the recon-all.log and recon-all-status.log, I couldn't figure out what the error is. Mon Aug 7 10:37:16 PDT 2006 [EMAIL PROTECTED] Intensity Normalization2 Mon Aug 7 10:37:16 PDT 2006 [EMAIL PROTECTED] Mask BFS Mon Aug 7 11:01:39 PDT 2006 [EMAIL PROTECTED] WM Segmentation Mon Aug 7 11:01:59 PDT 2006 Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 .. [EMAIL PROTECTED] Mask BFS Mon Aug 7 11:01:39 PDT 2006 /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 Talairach transform /usr/local/freesurfer/subjects/td21new/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/mri/transforms/talairach.xfm writing masked volume to brain.finalsurfs.mgz... # [EMAIL PROTECTED] WM Segmentation Mon Aug 7 11:01:59 PDT 2006 \n cp wm.mgz wm.seg.mgz \n \n mri_segment -keep brain.mgz wm.seg.mgz \n preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: 105.9 +- 5.5 [80.0 --> 125.0] GM: 70.1 +- 9.7 [30.0 --> 96.0] setting bottom of white matter range to 79.7 setting top of gray matter range to 89.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4126 sparsely connected voxels removed... thickening thin strands 20 segments, 2519 filled 2784 bright non-wm voxels segmented. 2121 diagonally connected voxels added... white matter segmentation took 10.4 minutes writing output to wm.seg.mgz... Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 Thanks -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Would adjusting watershed parameters change pial surface?
I was wondering if setting the watershed parameters higher and rerunning autorecon2 would expand the pial surface line if the outer rim of the brain is being left out? Or would this not fix the problem? Thanks -- -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Queue tasks?
I was wondering if it is possible to queue up various subjects like if the computers were going to be left for several days to run autorecon1 and 2 on a subject, and when that finishes move on to the next subject etc. If it is not possible in freesurfer has anyone written a script that I could use to do this kind of thing? Thanks -- -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Expanding pial outline
I ran two brains through autorecon2 and the pial line is drawn too close at many parts and cuts off parts of the brain. I looked through the website and only saw instructions for how to remove stuff and make the pial line smaller. I was wondering if there is a command I can run to expand the pial line or what is the best way to edit the files so more brain is included. I was looking at the threshold tools and couldn't see a way to convert say anything with a value of 30-40 to 60, so I was wondering if that was also possible. Thanks -- -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question concerning orientation
I have run several instances of autorecon2 and have only got left hemisphere data. The log file says that autorecon finished with errors but I can not find where to find these errors. I believe that the problem is the way the data being fed in is oriented so I was wondering how I should reorient it to get it to work. Thanks Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
