Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hi Alexandra, Thanks for your email. We have identified the problem an it will be fixed for the next build of our development version. 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: Z K zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Cc: e iglesias e.igles...@bcbl.eu Sent: Thursday, August 20, 2015 2:29:16 PM Subject: 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
Re: [Freesurfer] FS 6.0 dev for Mac?
The freesurfer Lion build has been tested and works for all OSX platforms up to Yosemite. -Zeke On Aug 21, 2015, at 5:32 AM, lukas.sch...@ukb.uni-bonn.de wrote: Hi Freesurfer team! I wonder if the newest FS version (6.0) is available for a more recent MacOs Version than Lion... Best wishes, Luke ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Query about transformations in the recon-all
we use a procedure from Avi Snyder to compute (but not apply) a 12 degree of freedom transform to MNI space. This is available for coordinate reporting and we use it a bit for things like finding the approximate center of the brain cheers Bruce On Wed, 19 Aug 2015, chenhf_uestc wrote: Hi, Bruce Thanks for your reply. Another question is What is talairach transformationprocedure (This computes the affine transform from the orig volume to the M NI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer scrip t called talairach). Why I need to transform from native space to MNI305 (We perform recon-all in the native space)? Best, Feng 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2015-08-18 22:09 主题：Re: [Freesurfer] Query about transformations in the recon-all 收件人：Freesurfer support listfreesurfer@nmr.mgh.harvard.edu 抄送： Hi Feng we compute many transforms for many reasons. The em reg is computed once in the image with skull to help with skull stripping, then again to the GCA atlas to initialize the nonlinear transform for computing the aseg segmentation. cheers Bruce On Tue, 18 Aug 2015, chenhf_uestc wrote: Dear Freesurfer experts, I have some questions in the recon-all. After reading online manual and d iscussing with the experts in the maillist, I have known all the recon-all procedures performed in the ?? ?individual native space. However, I very confuse that there are many transformations in the recon- all, e.g., 1. talairach transformation (This computes the affine transform from the orig volume t o the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer scr ipt called talairach), why I need transform from native space to MNI305; 2. EM (GCA) Registration (Com putes transform to align the mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/avera ge). What is the GCA atlas? what is the usage of this atlas? 3. CA Register (Computes a nonlinear tra nsform to align with GCA atlas. Creates the file mri/transform/talairach.m3z). Why we should align with GCA atlas? This transform is nonlinear, and what is the transform in the EM (GCA) Registr ation (Affine? 12 dof?); 4. EM Registration, with Skull (Computes transform to align volume mri/nu_no neck.mgz with GCA volume possessing the skull); Is there any detailed documentation in the online manual to introduce the se transformation? Could anyone give me a website? Any help would be greatly appreciate. Best, Feng ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly 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] Question about Talairach
HiLauren, This should be the correct command: freeview -v tal_before/mri/T1.mgz -v tal_before/mri/brainmask.mgz:reg=transforms/talairach.xfm (so remove the part 001/mri/ before transforms). Best, Koene ___ 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] check Talairach registration using Freeview
Thanks for your reply Doug. The flag -v that you suggested is indeed required, but I found out that it's not: freeview -v subj1/mri/T1.mgz -v subj1/mri/brainmask.mgz:reg=subj1/mri/transforms/talairach.xfm But that this seemed to work: freeview -v subj1/mri/T1.mgz -v subj1/mri/brainmask.mgz:reg=/transforms/talairach.xfm I believe the brain is in then Talairach atlas space (although the command line window still says ERROR: could not read transforms/talairack.xfm). Two followup questions: 1. This supposedly gives the brain of my subject in Talairach space but I still need a Talairach reference as well to see how well the transform for this person worked. Can you tell me where I can find the (or a) FS Talairach brain to also load into Freeview? 2. Is there a way to save the brain mask of this subject in Talairach space? ~Koene ___ 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-based Cluster Summary Table as created by mri_glmfit-sim
Some widespread clusters don't appear to be localized the place where is the vertex with the maximum sig. Best regards, Matthieu Le 21 août 2015 20:01, Douglas Greve gr...@nmr.mgh.harvard.edu a écrit : It is based on the vertex with the maximum sig. What do you mean it does not fit well? On 8/19/15 1:25 PM, Matthieu Vanhoutte wrote: Hello Freesurfer's experts, I used the group analysis clusterwise correction with glmfit-sim and I found that Annot field in Cluster Summary Table don't always fit well with the corresponding region on ?h.aparc.a2009s.annot file. How is determined precisely each localization of each cluster in the summary table ? Thanks in advance ! Best regards, Matthieu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Surface-based Interhemispheric Registration : Compare left vs. right patients
xhemireg seems to create e.g. left symmetric surface of the right normal one. Once xhemi/surf/lh.pial has been created and surface data surf/rh.overlay.mgh copied into xhemi/surf/lh.overlay.mgh, why don't register surf/lh.overlay.mgh and xhemi/surf/lh.overlay onto fsaverage lh.pial surface ? Best regards, Matthieu Le 21 août 2015 19:49, Douglas Greve gr...@nmr.mgh.harvard.edu a écrit : Sorry, what is the problem? Is sounds like xhemi should be apprpriate for your application. fsaverage is not symmetric and will lead to biased results. On 8/20/15 9:27 AM, Matthieu Vanhoutte wrote: 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 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 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] selxavg3-sess error
I thought this problem was fixed when you eliminated the multiple formats (?) On 8/20/15 12:03 PM, Rodriguez-Thompson, Anais wrote: 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
Re: [Freesurfer] Surface-based Cluster Summary Table as created by mri_glmfit-sim
It is based on the vertex with the maximum sig. What do you mean it does not fit well? On 8/19/15 1:25 PM, Matthieu Vanhoutte wrote: Hello Freesurfer's experts, I used the group analysis clusterwise correction with glmfit-sim and I found that Annot field in Cluster Summary Table don't always fit well with the corresponding region on ?h.aparc.a2009s.annot file. How is determined precisely each localization of each cluster in the summary table ? Thanks in advance ! Best regards, Matthieu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] F test results
You need to use 1 -1 0 0 1 0 -1 0 On 8/19/15 11:38 AM, Lim, Lena wrote: Dear experts, I have 3 groups (A, PC, HC) and IQ as cov and I tried to do a F test on the cortical thickness but the output doesn't make sense as it covered the whole brain (please see attached). I used the following commands: mris_preproc --fsgd 3gps_IQ.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.3gps_IQ.thickness.10.mgh mri_glmfit --y lh.3gps_IQ.thickness.10.mgh --fsgd 3gps_IQ.fsgd doss --C 3gps_IQ_Ftest.mtx --C 3gps_IQ_AbusedmorethanHC.mtx --C 3gps_IQ_AbusedmorethanPC.mtx --C 3gps_IQ_PCmorethanHC.mtx --surf fsaverage lh --cortex --glmdir lh.3gps_IQ_thickness mri_glmfit-sim --glmdir lh.3gps_IQ_thickness --cache 2 abs --cwp 0.05 --2spaces F contrast: 1 -1 0 0 0 0 -1 0 What went wrong? Please kindly help... Many thanks, Lena -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 04 August 2015 19:52 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] contrasts The F would be 1 -1 0 0 0 0 -1 0 Your t-contrasts are correct (you don't need to do both directions) On 08/03/2015 03:40 PM, Lim, Lena wrote: Hi experts, I have 3 groups: (A, PC and HC) and 1 covariate: IQ. For a DOSS file, how should I define the F contrast? Would it still be: I -1 0 ? 1 0 -1 And would the t contrast for say APC be: 1 -1 0 0 and for A PC be -1 1 0 0 etc Many thanks, Lena ___ 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 ___ 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] check Talairach registration using Freeview
try freeview -v subj1/mri/T1.mgz -v subj1/mri/brainmask.mgz:reg=subj1/mri/transforms/talairach.xfm On 8/17/15 5:49 PM, Koene Van Dijk wrote: Hi there, I have two questions regarding Talairach registration. _*Question 1:*_ I would like to check Talairach registration according to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview I see this line for the tutorial: freeview -v tal_before/mri/T1.mgz tal_before/mri/brainmask.mgz:reg=tal_before/mri/transforms/talairach.xfm And I tried to apply that to my subject: freeview -v subj1/mri/T1.mgz subj1/mri/brainmask.mgz:reg=subj1/mri/transforms/talairach.xfm Freeview opens and I see the T1 but it gives an error for the brain mask: Failed to load MRI: fullpath/subj1/mri/brainmask.mgz Does anybody know what's going wrong? _*Question 2:*_ Another way to do it would be to move the brainmask.mgz file into Talairach space and save it and then load that volume (let's call it brainmask_moved_to_tal.mgz) onto the FS Talairach subject. 2a: How do I move brainmask.mgz using subj1/mri/transforms/talairach.xfm and save the output? 2b: Where do I find the FS Talairach brain? I'm looking for the underlay that I see when I run: tkregister2 --s subj1 --fstal --surfs (as per instructions here: http://freesurfer.net/fswiki/eTIV) Thanks for any insights! Koene ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FDR cluster-level Correction
On 8/20/15 7:49 AM, Meiling Li wrote: 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? mri_binarize with the --fdg option. run with --help to get more info 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. It is much, much faster to use the --cache instead of --sim (cache uses precomputed values). the only reason you would want to do your own is in case you have a different mask (ie, not whole cortex). If you want to do this, it is better/faster to use mri_mcsim instead of mri_glmfit-sim Thank you very much! Meiling 宝宝的进口奶粉纸尿 裤，1元全包了 http://r.mail.163.com/r.jsp?url=http%3A%2F%2F1.163.com%2Fsearch.do%3Fkeyword%3D%25E6%25AF%258D%25E5%25A9%25B4%26from%3Dfooter_baby1sign=2120126086_r_ignore_statId=7_13_79_46_r_ignore_uid=n...@163.com 宝宝的进口奶粉纸尿裤，1元 全包了 http://r.mail.163.com/r.jsp?url=http%3A%2F%2F1.163.com%2Fsearch.do%3Fkeyword%3D%25E6%25AF%258D%25E5%25A9%25B4%26from%3Dfooter_baby1sign=2120126086_r_ignore_statId=7_13_79_46_r_ignore_uid=n...@163.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] selxavg3-sess error
Hi Doug, Sorry I wasn't clear. That was a separate issue. I was using a different analysis (SIRP_LoadRegression_Stable5_050514) that uses an old per-session file that was generated in 5.0 (fmc.sm5.nii). For the current analysis (SIRP_LoadRegression_Stable5_072915), I want to run the analysis per-run. Running preproc I get an fmcpr.nii.gz file, but I don't get the fmcpr.sm5.nii.gz file, which the analysis looks for. Best, Anais From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, August 21, 2015 1:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error I thought this problem was fixed when you eliminated the multiple formats (?) On 8/20/15 12:03 PM, Rodriguez-Thompson, Anais wrote: 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
Re: [Freesurfer] fast_selxavg3 ( ) failed\n
Do you have matlab installed? If so, is it in your path? On 8/18/15 4:54 PM, Gay,Charles Wysaw wrote: Hi - I've encountered an error in step 8 of the functional connectivity analysis. here is some of the information requested with errors: FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 - Please include the following additional information in your report: 1) subject name: B113v1 2) the entire command-line executed: selxavg3-sess -s B113v1 -a fc.linsulaseed.surf.lh %step 7 code was: mkanalysis-sess -analysis fc.linsulaseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Insula.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR 2 -per-session %which completed successfully 3) the error message generated :Started at Wed Aug 12 12:56:41 EDT 2015 Ended at Wed Aug 12 13:11:49 EDT 2015 preproc-sess done --- /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1 Wed Aug 12 13:11:50 EDT 2015 anadir = /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/fc.linsulaseed.surf.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output matlab: Command not found. -- ERROR: fast_selxavg3() failed\n 4) optionally include the subject's /script/recon-all.log: I included the recon-all.log and selxavg3-sees-rest-fc...log On A previous post I saw the command which matlab was asked: below is the result when I entered it:which matlab matlab: Command not found. Thanks for assistance, chaz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] check Talairach registration using Freeview
actually the error in the command line window is: Not reading in xfm fileinfo ___ 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] check Talairach registration using Freeview
Koene, can you give the full command line and the full terminal output? I can't remember what was in your previous email (and I've deleted it:) doug On 8/21/15 5:20 PM, Koene Van Dijk wrote: actually the error in the command line window is: Not reading in xfm fileinfo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Surface-based Cluster Summary Table as created by mri_glmfit-sim
Can you upload an example (with vertex numbers)? On 8/21/15 3:37 PM, Matthieu Vanhoutte wrote: Some widespread clusters don't appear to be localized the place where is the vertex with the maximum sig. Best regards, Matthieu Le 21 août 2015 20:01, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu a écrit : It is based on the vertex with the maximum sig. What do you mean it does not fit well? On 8/19/15 1:25 PM, Matthieu Vanhoutte wrote: Hello Freesurfer's experts, I used the group analysis clusterwise correction with glmfit-sim and I found that Annot field in Cluster Summary Table don't always fit well with the corresponding region on ?h.aparc.a2009s.annot file. How is determined precisely each localization of each cluster in the summary table ? Thanks in advance ! Best regards, Matthieu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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-based Interhemispheric Registration : Compare left vs. right patients
On 8/21/15 3:47 PM, Matthieu Vanhoutte wrote: xhemireg seems to create e.g. left symmetric surface of the right normal one. Once xhemi/surf/lh.pial has been created and surface data surf/rh.overlay.mgh copied into xhemi/surf/lh.overlay.mgh, Yes, both the lh and the rh are registered to the lh symmetric surface. Though it has an lh designation, the hemi is meaningless because it symmetric. Why does this not work for your data? why don't register surf/lh.overlay.mgh and xhemi/surf/lh.overlay onto fsaverage lh.pial surface ? because fsaverage is not symmetric. Best regards, Matthieu Le 21 août 2015 19:49, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu a écrit : Sorry, what is the problem? Is sounds like xhemi should be apprpriate for your application. fsaverage is not symmetric and will lead to biased results. On 8/20/15 9:27 AM, Matthieu Vanhoutte wrote: 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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] FS 6.0 dev for Mac?
Hi Freesurfer team! I wonder if the newest FS version (6.0) is available for a more recent MacOs Version than Lion... Best wishes, Luke___ 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.
