Re: [Freesurfer] cross and long in qdec
Hi P Qdec cannot do a longitudinal analysis, nor can it mix cross and long. For that you need to use the LME Matlab tools that come with freesurfer. You could also do a 2stage analysis of change in qdec for all subjects with 2 time points and you can of course always do a cross sectional analysis of baseline data. I would recommend the LME tools. Also note you need to run the single time point subjects through the longitudinal stream (-base and -long) to make them compatible . Best Martin On Aug 20, 2015 2:28 AM, prasser pras...@zoho.com wrote: Hi, If I have a set of subjects from a study collected at time 0 (T0) and a subset of these subjects that also have data collected at time 1 (T1), can I run qdec on the T0 subject's with no T1 together with the longs of the subject's at T0 that have a T1? Thanks, P ___ 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] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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
Re: [Freesurfer] Trakula
Hi Anastasia, please find the files in attachment. Best regards Bahram 2015-08-19 21:55 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote: Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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. anat2diff.bbr.mat Description: application/extension-mat anat2mni.mat Description: application/extension-mat ___ 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] surface lines in manual edits
Hi Freesurfer experts, I asked this question yesterday. I ended up seeing that a similar question had been asked in July, and spoke to the asker of the question, who told me his problem had been zeroes on the control point dat file, for several points. I have attempted to go back through these, and reran several subjects with such zeroes removed, however - the same problem reoccurs with the white matter surface being seen as the brain surface. Any help would be welcomed. Thank you. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Kriegel, Jennifer Lynn Sarai Sent: Wednesday, August 19, 2015 10:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] surface lines in manual edits Hi, I'm hand editing brains to get the most accurate cortical thickness analysis possible, and ran into a bit of a problem with surface lines. One issue is with the original structural reconstructions from the hdr files, and the other deals with the manual edits I've made when the recon was re-run. 1. A couple of the volumes initially had the white matter surface as the pial surface/cortical surface. Initially I tried running g-cut for some of the suggestions I found on the wiki when the surface lines are off. This didn't work on those problem volumes. 2. When editing with control points in order to get the white matter areas that were not incorporated into the white matter surface included, the control points have overcoverected and made the same issue that was the occurrence with the two or three original volumes - the white matter surface is seen as the brain/pial surface. I was conservative with these as well. I have been looking on the wiki for a way to adjust the actual surface lines manually based on the actual white matter/brain surface. I think this would be most useful, but I'm not sure if it is possible. If so, how could this be done - and, if not, what possible way of trouble shooting can help deal with this white matter as pial surface issue? Best regards, - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edumailto:jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ 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] FDR cluster-level Correction
Hi Freesurfer experts I am doing FS-nonlinear volume based FC analysis with cluster-level correction. 1. Could you please point me which command can do the FDR cluster-level Correction? 2. If i do correction using MonteCalo cluster-based correction. Is it right like the following command mri_glmfit-sim --glmdir g2v0 --sim mc-z 1 1.3 mc-z 1.3 --cwp 0.05 --sim-sign abs. It seems that the MonteCalo cluster-based correction costs long long time. Thank you very much! Meiling 宝宝的进口奶粉纸尿裤，1元全包了___ 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] TRACULA: Could not find satisfactory control point fit - try 20786
Hi Anastasia, I have been having difficulty running the trac-all -prep command on one subject (all of my other subjects have been fine), and it appears that the process gets stuck once processing for pathway 8 begins, and cannot find satisfactory control points. However, I was out of town and left the command running, and came back to find that trac-preproc finished without error. Upon review of the log file, it appears that after 20786 tries, either control points for pathway 8 were established, or the preprocessing simply moved on to pathway 9, and was able to successfully complete. I am unable to attach the entire log file here, but have copied and pasted a small section with the errors below (from try 20784 - 20786). In try 20786, file writing begins, but then I see the following messages: INFO: Rejected 94 streamlines for straying off mask INFO: Rejected 6 streamlines for reversing direction INFO: Rejected 48 streamlines as length outliers I'm concerned that pathway 8 did not, in fact, process successfully, and I was wondering if you have any suggestions here. I am also wondering what this may mean for the other pathways for this subject, and how this may affect my data after bedpost and trac-all -path. Please advise on any suggestions you have. Thank you for your help, Michelle WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels WARN: Turning off overlap check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 105 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 13 INFO: Minimum allowable curvature at a dominant point is 0.0647175 INFO: Points where local peeks in curvature occur are 106 165 103 (curv = 0.136434) 109 156 97 (curv = 0.0996267) 89 142 87 (curv = 0.092719) 70 156 100 (curv = 0.112663) 74 166 104 (curv = 0.138384) INFO: Intermediate dominant points are 104 187 99 106 165 103 91 142 87 74 166 104 78 182 97 INFO: Final dominant points are 104 187 99 106 165 103 70 154 99 74 166 104 78 182 97 WARN: Defaulting to equidistant control points INFO: Selected control points are 104 187 99 107 162 102 91 142 87 70 158 101 78 182 97 INFO: Distances between consecutive points are 25 30 30 26 INFO: Selected control points in test subject's space are 139 191 42 142 167 42 128 150 35 109 162 41 115 185 41 INFO: Distances between consecutive points in test subject's space are 24 23 23 24 WARN: Could not find satisfactory control point fit - try 20785 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels WARN: Turning off overlap check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 12 INFO: Minimum allowable curvature at a dominant point is 0.0590185 INFO: Points where local peeks in curvature occur are 107 152 96 (curv = 0.0988129) 84 145 87 (curv = 0.0815938) 67 156 96 (curv = 0.128644) 73 168 108 (curv = 0.162002) INFO: Intermediate dominant points are 96 176 119 107 152 96 85 145 87 73 168 108 70 184 108 INFO: Final dominant points are 96 176 119 107 152 96 67 157 97 73 168 108 70 184 108 WARN: Defaulting to equidistant control points INFO: Selected control points are 96 176 119 107 157 100 87 144 87 68 159 98 70 184 108 INFO: Distances between consecutive points are 29 27 27 27 INFO: Selected control points in test subject's space are 132 177 50 142 163 41 125 152 35 107 163 40 108 185 45 INFO: Distances between consecutive points in test subject's space are 19 21 22 23 WARN: Could not find satisfactory control point fit - try 20786 Writing output files to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/mni/fminor_PP_avg33_mni_bbr_* Writing spline volume to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/mni/fminor_PP_avg33_mni_bbr_cpts_5.nii.gz Writing spline volume to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.nii.gz Done in 8115.17 sec. Loading streamline start ROI from /opt/freesurfer/trctrain/trc001/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc001/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from /opt/freesurfer/trctrain/trc001/dlabel/mni/lh.atr_PP.bbr.trk Loading streamline start ROI from /opt/freesurfer/trctrain/trc002/dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz Loading streamline end ROI from /opt/freesurfer/trctrain/trc002/dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz Loading streamlines from
Re: [Freesurfer] Segmentation in dev version
Hi Lee Thank you for your response. I have a follow up question- After running recon-all -all, I found the parahippocampal cortex and entorhinal cortex under two files- wmparc.mgz and aparc+ages.mgz. What is the difference between the two? Also, I haven't been able to find perirhinal cortex under any of the files. I wonder why? On Mon, Aug 3, 2015 at 5:22 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu wrote: Hi Priyanka, These are all automatically created automatically by running recon-all -all. Best, Lee On Sat, 1 Aug 2015, Priyanka Mehta wrote: Hi Please excuse my extremely basic question. I would like to perform segmentation on my T1 image to obtain the following: a. Entorhinal Cortex b. Perirhinal Cortex c. Parahippocampal Cortex Is there a specific command I should be using in the 6.0 dev version? Or should I just be using recon-all -all ? Best, Priyanka Mehta ___ 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] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Zeke and Eugenio, Thanks for your quick answers. I removed the maverick distribution and installed the lion one pointed by Zeke. Running the segmentation, I get the same message as before: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Here is were the symbolic link is pointing: segmentSubjectT1_autoEstimateAlveusML - ../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a It is pointing to a directory which is outside of freesurfer's. -Alexandra On 8/20/15 9:38 AM, Z K wrote: Hi Alexandra, The mavericks build that you downloaded was an experimental build that hasnt been updated for awhile. Please remove that version and download and install the lion version instead. That version is more up-to-date. Sorry for the confusion. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/20/2015 04:42 AM, Eugenio Iglesias wrote: Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Surface-based Interhemispheric Registration : Compare left vs. right patients
Dear FS experts, I have shown in mailing list and xhemi commands as explained here, a beginning of a solution to my problem : http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi However, I didn't understand all the steps needed in may case. I have patients with unilateralized problem on left or right hemisphere. But, I would like to statistically compare left vs right hemisphere groups. So, I think xhemi should help me to register for example both hemispheres of my right lateralized patients onto symmetrical template ? I have already registered my surface data of all patients on fsaverage template. Couldn't it be possible to apply Xhemi transformation on fsaverage surface data of all right lateralized patients ? What are the steps to do it ? Many thanks in advance for helping ! Best regards, Matthieu ___ 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] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Ah, I see. This issue must have arisen due to some changes I made in the freesurfer git repository. Eugenio, I should have this resolved by tomorrows build. Alexandra, thanks for pointing this out. It should be fixed in tomorrows daily build. Ill send you an email to confirm. -Zeke Hi Zeke and Eugenio, Thanks for your quick answers. I removed the maverick distribution and installed the lion one pointed by Zeke. Running the segmentation, I get the same message as before: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Here is were the symbolic link is pointing: segmentSubjectT1_autoEstimateAlveusML - ../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a It is pointing to a directory which is outside of freesurfer's. -Alexandra On 8/20/15 9:38 AM, Z K wrote: Hi Alexandra, The mavericks build that you downloaded was an experimental build that hasnt been updated for awhile. Please remove that version and download and install the lion version instead. That version is more up-to-date. Sorry for the confusion. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/20/2015 04:42 AM, Eugenio Iglesias wrote: Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] visualizing paths stats by voxel
Hi Janosch - Indeed, someone has to be first. I'll send you a fresh build of dmri_paths tomorrow. You'll have to replace your copy of $FREESURFER_HOME/bin/dmri_paths with it and then rerun trac-all -path only for the subjects that have 1 time point. Then rerun trac-all -stat with all subjects together. And then tell us what other problem you find :) Best, a.y On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote: Hey Anastasia, Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - There is a bug in how the output paths are saved when longitudinal TRACULA is run with one time point only. I'm working on a fix. OK, then I'm relieved that it isn't an error on my side. Thank you very much for looking into it! In the meantime, you can try your analysis with the subjects that have multiple time points and you won't be affected by this problem. I can see that the subjects with a single time point are about 1/3 of your sample, and so you may not want to drop them completely. Yeah, it's children's data, so I'm happy about every measurement we got. I'll be waiting for the fixed script to be able to include all subjects in the analysis... Thank you for trying things that nobody else has tried and finding these bugs! Somebody has to be the first, eh? :) Thank you very much, Janosch More soon, a.y On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: Hey Anastasia, thanks for looking into this. Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Looking at the stats files of your subjects, just by a quick count of the number of lines, I see that there are some subjects that have only 1 time point and some that have multiple time points, and that the pathstats.byvoxel.txt files have different lengths between those two types of subjects. I suspect that the strange average path that you get has to do with how this mixing of subjects was done. Did you run the subjects with a single time point through the longitudinal stream as well? Yes, I ran the longitudinal stream for all subjects, also for the ones with only one time point. Thanks, Janosch Best, a.y On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia, yes, I am. But it looks similar in the distributed version :( Thanks, Janosch Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Are you by any chance using the dev version of freeview? a.y On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia and list, I'm trying to do analyses along the tract with the path_stats_byvoxel files. When I am visualizing the points using the waypoint functionality of Freeview, it looks a little strange, i.e., the points are not equally spaces on the tract, but clumped together at some parts and spread out on others, see: this looks different to your slides: Also, the most posterior points seem to be strangely located (in the other hemisphere). What could be the reason for this strange behavior? Thanks, Janosch 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] FreeSurfer 6.0 dev version Output
This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is
this a bug in the dev version?
On Aug 20, 2015, at 3:20 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu wrote:
It seems that the command:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in
lh.hippoSfLabels-T1.v10.mgz. You can run:
mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
and then the correct label names from the Lookup Table will show up.
Best,
Lee
On Thu, 20 Aug 2015, Priyanka Mehta wrote:
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns correctly.
However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels only' checked,
the lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Prya,
that is because MriCron is not that great at overlaying images that are
in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the
output. FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel space as T1.nii,
and should be properly overlayed
by MriCron. However, the resolution of the segmentation will be 1 mm,
rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
alignment is not correct (see attached
picture).
I wonder what is causing this issue? Since the CA1 was extracted from
the same T1 image, they should
technically be in the same space and therefore should align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from
the previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are
interested in CA1 (label 206), you can
run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in
the 6.0 dev version.
I used the following command:
Re: [Freesurfer] Trakula
Hi Bahram - The anatomical-to-diffusion registration matrix is all zeros, so something went wrong there. I'll need to see all the output files to investigate. Can you please zip up this subject's tracula output directories (dmri, dmri.bedpostX, dpath, dlabel, scripts) and upload everything for me here? https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks, a.y On Thu, 20 Aug 2015, B M wrote: Hi Anastasia, please find the files in attachment. Best regards Bahram 2015-08-19 21:55 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote: Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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
Re: [Freesurfer] TRACULA: Could not find satisfactory control point fit - try 20786
Hi Michelle - It sounds like there is something wrong with this subject that affects a part of the brain that the forceps minor of the corpus callosum goes through. It could be a piece of the brain mask missing, or poor segmentation of the T1, or poor T1-to-diffusion registration. Can you look at the FA map (dmri/dtifit_FA) and the T1 segmentation in diffusion space (dlabel/diff/aparc+aseg) to see if anything looks wrong? Thanks, a.y On Thu, 20 Aug 2015, Michelle T Kassel wrote: Hi Anastasia, I have been having difficulty running the trac-all -prep command on one subject (all of my other subjects have been fine), and it appears that the process gets stuck once processing for pathway 8 begins, and cannot find satisfactory control points. However, I was out of town and left the command running, and came back to find that trac-preproc finished without error. Upon review of the log file, it appears that after 20786 tries, either control points for pathway 8 were established, or the preprocessing simply moved on to pathway 9, and was able to successfully complete. I am unable to attach the entire log file here, but have copied and pasted a small section with the errors below (from try 20784 - 20786). In try 20786, file writing begins, but then I see the following messages: INFO: Rejected 94 streamlines for straying off mask INFO: Rejected 6 streamlines for reversing direction INFO: Rejected 48 streamlines as length outliers I'm concerned that pathway 8 did not, in fact, process successfully, and I was wondering if you have any suggestions here. I am also wondering what this may mean for the other pathways for this subject, and how this may affect my data after bedpost and trac-all -path. Please advise on any suggestions you have. Thank you for your help, Michelle WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels WARN: Turning off overlap check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 105 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 13 INFO: Minimum allowable curvature at a dominant point is 0.0647175 INFO: Points where local peeks in curvature occur are 106 165 103 (curv = 0.136434) 109 156 97 (curv = 0.0996267) 89 142 87 (curv = 0.092719) 70 156 100 (curv = 0.112663) 74 166 104 (curv = 0.138384) INFO: Intermediate dominant points are 104 187 99 106 165 103 91 142 87 74 166 104 78 182 97 INFO: Final dominant points are 104 187 99 106 165 103 70 154 99 74 166 104 78 182 97 WARN: Defaulting to equidistant control points INFO: Selected control points are 104 187 99 107 162 102 91 142 87 70 158 101 78 182 97 INFO: Distances between consecutive points are 25 30 30 26 INFO: Selected control points in test subject's space are 139 191 42 142 167 42 128 150 35 109 162 41 115 185 41 INFO: Distances between consecutive points in test subject's space are 24 23 23 24 WARN: Could not find satisfactory control point fit - try 20785 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels WARN: Turning off overlap check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 12 INFO: Minimum allowable curvature at a dominant point is 0.0590185 INFO: Points where local peeks in curvature occur are 107 152 96 (curv = 0.0988129) 84 145 87 (curv = 0.0815938) 67 156 96 (curv = 0.128644) 73 168 108 (curv = 0.162002) INFO: Intermediate dominant points are 96 176 119 107 152 96 85 145 87 73 168 108 70 184 108 INFO: Final dominant points are 96 176 119 107 152 96 67 157 97 73 168 108 70 184 108 WARN: Defaulting to equidistant control points INFO: Selected control points are 96 176 119 107 157 100 87 144 87 68 159 98 70 184 108 INFO: Distances between consecutive points are 29 27 27 27 INFO: Selected control points in test subject's space are 132 177 50 142 163 41 125 152 35 107 163 40 108 185 45 INFO: Distances between consecutive points in test subject's space are 19 21 22 23 WARN: Could not find satisfactory control point fit - try 20786 Writing output files to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/mni/fminor_PP_avg33_mni_bbr_* Writing spline volume to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/mni/fminor_PP_avg33_mni_bbr_cpts_5.nii.gz Writing spline volume to /home/msabri/Conn_Age/DTI/tracula/5152.fs/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.nii.gz Done in 8115.17 sec. Loading streamline start ROI from
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
It seems that the command:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in
lh.hippoSfLabels-T1.v10.mgz. You can run:
mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
and then the correct label names from the Lookup Table will show up.
Best,
Lee
On Thu, 20 Aug 2015, Priyanka Mehta wrote:
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns correctly.
However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels only' checked, the
lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Prya,
that is because MriCron is not that great at overlaying images that are
in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel space as T1.nii,
and should be properly overlayed
by MriCron. However, the resolution of the segmentation will be 1 mm,
rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
alignment is not correct (see attached
picture).
I wonder what is causing this issue? Since the CA1 was extracted from the
same T1 image, they should
technically be in the same space and therefore should align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are
interested in CA1 (label 206), you can
run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the
6.0 dev version.
I used the following command: recon-all -i ${subject}.nii -subject
${subject} -all
-hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command:
freeview -v nu.mgz -v
lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is
Re: [Freesurfer] visualizing paths stats by voxel
Hey Anastasia, Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - There is a bug in how the output paths are saved when longitudinal TRACULA is run with one time point only. I'm working on a fix. OK, then I'm relieved that it isn't an error on my side. Thank you very much for looking into it! In the meantime, you can try your analysis with the subjects that have multiple time points and you won't be affected by this problem. I can see that the subjects with a single time point are about 1/3 of your sample, and so you may not want to drop them completely. Yeah, it's children's data, so I'm happy about every measurement we got. I'll be waiting for the fixed script to be able to include all subjects in the analysis... Thank you for trying things that nobody else has tried and finding these bugs! Somebody has to be the first, eh? :) Thank you very much, Janosch More soon, a.y On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: Hey Anastasia, thanks for looking into this. Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Looking at the stats files of your subjects, just by a quick count of the number of lines, I see that there are some subjects that have only 1 time point and some that have multiple time points, and that the pathstats.byvoxel.txt files have different lengths between those two types of subjects. I suspect that the strange average path that you get has to do with how this mixing of subjects was done. Did you run the subjects with a single time point through the longitudinal stream as well? Yes, I ran the longitudinal stream for all subjects, also for the ones with only one time point. Thanks, Janosch Best, a.y On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia, yes, I am. But it looks similar in the distributed version :( Thanks, Janosch Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Are you by any chance using the dev version of freeview? a.y On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia and list, I'm trying to do analyses along the tract with the path_stats_byvoxel files. When I am visualizing the points using the waypoint functionality of Freeview, it looks a little strange, i.e., the points are not equally spaces on the tract, but clumped together at some parts and spread out on others, see: this looks different to your slides: Also, the most posterior points seem to be strangely located (in the other hemisphere). What could be the reason for this strange behavior? Thanks, Janosch 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
Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Alexandra, The mavericks build that you downloaded was an experimental build that hasnt been updated for awhile. Please remove that version and download and install the lion version instead. That version is more up-to-date. Sorry for the confusion. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/20/2015 04:42 AM, Eugenio Iglesias wrote: Hi Alexandra, that's weird. Where is the symbolic link pointing? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] selxavg3-sess error
Hi Doug, I sent a message a while back about a problem I was having running selxavg3 (I've attached the thread below this email). Selxavg3 is looking for a file that was not generated during preprocessing (fmcpr.sm5.nii.gz). The commands I was using were preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd bold -fwhm 5 -per-run mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm slopepar -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 5 -per-run I sent you a couple of logs, but did not hear back about how I can generate the fmcpr.sm5.nii file. In the meantime I haven't been able to run any first level analyses on my subjects. Is there any update to this issue? Any insight into the problem would be greatly appreciated! Thanks, Anais From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson, Anais [arodriguez-thomp...@mgh.harvard.edu] Sent: Thursday, July 30, 2015 6:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] selxavg3-sess error Hi Doug, Attached is doug2.log. Thanks, Anais From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, July 30, 2015 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error ok, still not sure what is happening. Can you try preproc-sess -debug -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_072915 | tee doug2.log and send me doug2.log On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote: Hi Doug, Below are the contents of doug.log: set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return foreach grp ( $grpdefs ) foreach grp ( ) goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#SearchPathList == 0 ) then if ( 0 == 0 ) then set SearchPathList = . ; set SearchPathList = . endif endif goto check_params_return ; goto check_params_return set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( . ) if ( ! -e $d ) then if ( ! -e . ) then set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( . ) set UniqueList = ( . ) end end set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( . ) set errs = 0 ; set errs = 0 set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( GDDA001 ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./GDDA001 if ( -d $stst ) then if ( -d ./GDDA001 ) then if ( ! -r $stst ) then if ( ! -r ./GDDA001 ) then pushd $stst /dev/null ; pushd ./GDDA001 set tmp = ( $tmp `$PWDCMD` ) ; set tmp = ( `$PWDCMD` ) pwd popd /dev/null ; popd endif endif end end set nfound = ( $#tmp ) ; set nfound = ( 1 ) if ( $nfound == 0 ) then if ( 1 == 0 ) then if ( $nfound 1 ) then if ( 1 1 ) then set SessPath = ( $SessPath $tmp ) ; set SessPath = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( ! $IsUnique ! $AllowRedundant ) then if ( ! 1 ! 0 ) then set UniqueList = ( $UniqueList $s ) ; set UniqueList = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) endif endif end end echo $SessPath echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 exit $errs ; exit 0 set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#analysis == 0 $flacfile == 0 ) then if ( 1 == 0 == 0 ) then if ( $#analysis != 0 ) then if ( 1 != 0 ) then if ( ! -d $analysis ) then if ( ! -d SIRP_LoadRegression_Stable5_072915 ) then if ( ! -e $analysis/analysis.info ) then if ( ! -e SIRP_LoadRegression_Stable5_072915/analysis.info ) then endif endif if ( $#flacfile != 0 ) then if ( 0 != 0 ) then if ( $perrun $jkrun ) then if ( 0 0 ) then if ( $UseOctave ) then if ( 0 ) then goto check_params_return ; goto check_params_return set StudyDir = `pwd` ; set StudyDir = `pwd` pwd if ( $#analysis ) then if ( 1 ) then set analysisname = $analysis set analysisname = SIRP_LoadRegression_Stable5_072915 set fsd = `getana -a $analysis -t fsd` ; set fsd = `getana -a $analysis -t fsd` getana -a
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns
correctly. However, when I view the segmentation with color map set to
Lookup Table and 'show existing labels only' checked, the lh.CA1.nii
segment shows as 128 Nerve label. Shouldn't it still be showing up as 206
CA1 label? I am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Prya,
that is because MriCron is not that great at overlaying images that are in
the same physical space but not in the same voxel space. You have two
options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
FreeView will correctly overlay the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call mri_extract_label. That volume
lives in the same voxel space as T1.nii, and should be properly overlayed
by MriCron. However, the resolution of the segmentation will be 1 mm,
rather than the 0.333 mm that you'd get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted the left CA1 using mri_extract_label
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
alignment is not correct (see attached picture).
I wonder what is causing this issue? Since the CA1 was extracted from the
same T1 image, they should technically be in the same space and therefore
should align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested
in CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the
6.0 dev version.
I used the following command: recon-all -i ${subject}.nii -subject
${subject} -all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command:
freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
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The information in this e-mail is intended only for the person to whom it
is
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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dispose of the e-mail.
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