Re: [Freesurfer] FW: Permutation output
Hi Doug, I am attaching the permutation log file. Thanks! Pablo Date: Mon, 17 Aug 2015 11:15:14 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Permutation output Can you send me the log file from the glmdir folder? The log file that has perm in the name? On 8/12/15 11:33 AM, pablo najt wrote: Will do that from now on. the output is as follow: This is the output I am getting which I believe is not what I need for check the permutation output C.dat F.mgh cnr.mgh gamma.mgh gammavar.mgh maxvox.dat sig.mgh Date: Wed, 12 Aug 2015 11:17:38 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Permutation output look in the folder of one of the contrasts (eg, rh-Diff-BD-HC-Intercept-sulc). Also, if you can paste such text into the email it is much more convenient for us than to sent us a tiff On 08/12/2015 11:12 AM, pablo najt wrote: Dear FS exp, In case my message got swamped, I am reposting my question. Many thanks! Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 11 Aug 2015 11:02:54 + Subject: Re: [Freesurfer] Permutation output Thanks. Sorry but I am not being able to figure it out yet. Basically I am not getting the expected outcome. So I thought to give you an idea of how I am running permutations. mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg And I am attaching a snapshot of the output files and the log of mdi_glmfit-sim. At this stage I am wondering whether in order to run permutation it is required use as input the output from fsgd rather than qdec, because my input is from qdec. Would this make any difference? Thanks. Pablo Date: Mon, 10 Aug 2015 11:13:13 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Permutation output It is the same thing, but the permutation output will have the name you gave the csdbase when you ran the simulation (ie, the 4th arg to --sim) On 08/10/2015 05:54 AM, pablo najt wrote: Thank you Doug. I run permutations with mdi_glmfit-sim --sim perm. Would you be able to advice on the output and how to open the permutation outputs? The tutorial instructs on how to open the *.summary file for the summary of clusters and *.sig.cluster.mgh the cluster corrected map, but not the permutation output. Thank you, Pablo Date: Fri, 7 Aug 2015 10:53:55 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running corrections for multiple comparisons. I am finding a fairly large cluster analyzing 2 groups on sulcal depth. However when I tried FDR or cluster wise correction the results do not seem to survive. As the result is on the region I was predicting I want to make sure there are no other options for correcting for multiple
Re: [Freesurfer] Trakula
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. Fri Aug 14 17:22:48 CEST 2015 /home/bm /usr/local/freesurfer/bin/trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc Subject P01-a SUBJECTS_DIR bmdaten/Auswertung/ALS-Review/Trakula/ FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 bm bm-linux Linux bm-linux 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 256954 maxlocks unlimited maxsignal256954 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 32909372 309815561927816 0 776952 25756624 -/+ buffers/cache:4447980 28461392 Swap:124999676 9000 124990676 Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
[Freesurfer] control points from cross transferred to long
Hi, On this page https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it mentions it is recommended to check if all CPs are accurately placed in the long. I was wondering what is the best way to do this? I know I can type in the RAS coordinates from the control.dat file and check each one this way, but this seems a little tedious and prone to errors especially as I can't paste into tkmedit. Also, is there a command that can get the intensity from brainmask.mgz from a given RAS coordinate? 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] license error
Hello, You say the .license file is in your applications folder but it's supposed to be located in your /Applications/freesurfer folder. If /Applications/freesurfer/.license does exist on your machine, than please make absolutely sure it exactly matches the email sent to you after you registered. Lastly, if neither of the above cases solves the problem, please send me your .license file *TO MY DIRECT EMAIL ADDRESS* (not the freesurfer list!) so I may examine it. Thanks. -Zeke On 08/18/2015 02:51 PM, Frank Kanayet wrote: Hi, I just installed freesurfer on my computer and included the license.txt film in the applications folder but when I tried to use the tkmedit bert orig.mgz to test the installation I received a message saying that ERROR: FreeSurfer license file /Applications/freesurfer/license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu http://surfer.nmr.mgh.harvard.edu/ to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. Can you help me figure out what is the mistake? Thanks, -- ** Frank J. Kanayet, Ph.D. Stanford University 420 Jordan Hall, Room 342 ** ___ 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] license error
Hi, I just installed freesurfer on my computer and included the license.txt film in the applications folder but when I tried to use the tkmedit bert orig.mgz to test the installation I received a message saying that ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. Can you help me figure out what is the mistake? Thanks, -- ** Frank J. Kanayet, Ph.D. Stanford University 420 Jordan Hall, Room 342 ** ___ 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] control points from cross transferred to long
In the dev version of freeview, you can go to File -Load Point set, and choose the control point file (shoulb be subject/tmp/control.dat) This allows you to flip through the points by entering the control point number or using an arrow to go to the next/previous control point in the file. This moves the cursor to the control point (which shows up as a green dot by default). You can also do the same thing to load them in the stable version of freeview, but there is no box to enter a control point number. If you move through the brain, you will see the control points as dots. Best, Lee On Mon, 17 Aug 2015, prasser wrote: Hi, On this page https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it mentions it is recommended to check if all CPs are accurately placed in the long. I was wondering what is the best way to do this? I know I can type in the RAS coordinates from the control.dat file and check each one this way, but this seems a little tedious and prone to errors especially as I can't paste into tkmedit. Also, is there a command that can get the intensity from brainmask.mgz from a given RAS coordinate? 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.
[Freesurfer] Using FreeSurfer Suggested Morphometry Sequences
Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ 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] fast_selxavg3 ( ) failed\n
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 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] control points from cross transferred to long
Hi P, if you want to investigate the control.dat file you can do so with freeview (File- Load Point Set and choose the control.dat file). In the dev version of Freeview there is an option to select a cp number or move through the list with arrows. In the stable version, there is no box, but you would still see the CP as white dots when scrolling through the brain. If you transfer the CP from cross, usually they should be accurately placed in the long, so a quick check is usually fine. Best, Martin On Aug 18, 2015, at 8:23 AM, prasser pras...@zoho.com wrote: Hi, On this page https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it mentions it is recommended to check if all CPs are accurately placed in the long. I was wondering what is the best way to do this? I know I can type in the RAS coordinates from the control.dat file and check each one this way, but this seems a little tedious and prone to errors especially as I can't paste into tkmedit. Also, is there a command that can get the intensity from brainmask.mgz from a given RAS coordinate? Thanks P ___ 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] Using FreeSurfer Suggested Morphometry Sequences
no, there is a post-hoc recon-all target you can use. -T2 or -T2pial or something. Sorry, I don't remember, maybe someone else can fill in the details Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into recon-all at the same time as the MEMPRAGE as a second series? best, John On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding dura cheers Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ 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 ___ 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] Using FreeSurfer Suggested Morphometry Sequences
Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into recon-all at the same time as the MEMPRAGE as a second series? best, John On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding dura cheers Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ 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
Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences
Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding dura cheers Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ 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] Query about transformations in the recon-all
Dear Freesurfer experts, I have some questions in the recon-all. After reading online manual and discussing 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 to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach), why I need transform from native space to MNI305; 2. EM (GCA) Registration (Computes transform to align the mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average). What is the GCA atlas? what is the usage of this atlas? 3. CA Register (Computes a nonlinear transform 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) Registration (Affine? 12 dof?); 4. EM Registration, with Skull (Computes transform to align volume mri/nu_noneck.mgz with GCA volume possessing the skull); Is there any detailed documentation in the online manual to introduce these 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 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
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 discussing 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 to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach), why I need transform from native space to MNI305; 2. EM (GCA) Registration (Computes transform to align the mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average). What is the GCA atlas? what is the usage of this atlas? 3. CA Register (Computes a nonlinear transform 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) Registration (Affine? 12 dof?); 4. EM Registration, with Skull (Computes transform to align volume mri/nu_noneck.mgz with GCA volume possessing the skull); Is there any detailed documentation in the online manual to introduce these 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 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] Permutation output
The log file ends abruptly. Try the following mri_glmfit-sim --debug --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg | tee doug.log and send me doug.log doug On 08/11/2015 07:02 AM, pablo najt wrote: Thanks. Sorry but I am not being able to figure it out yet. Basically I am not getting the expected outcome. So I thought to give you an idea of how I am running permutations. mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg And I am attaching a snapshot of the output files and the log of mdi_glmfit-sim. At this stage I am wondering whether in order to run permutation it is required use as input the output from fsgd rather than qdec, because my input is from qdec. Would this make any difference? Thanks. Pablo Date: Mon, 10 Aug 2015 11:13:13 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Permutation output It is the same thing, but the permutation output will have the name you gave the csdbase when you ran the simulation (ie, the 4th arg to --sim) On 08/10/2015 05:54 AM, pablo najt wrote: Thank you Doug. I run permutations with mdi_glmfit-sim --sim perm. Would you be able to advice on the output and how to open the permutation outputs? The tutorial instructs on how to open the *.summary file for the summary of clusters and *.sig.cluster.mgh the cluster corrected map, but not the permutation output. Thank you, Pablo Date: Fri, 7 Aug 2015 10:53:55 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running corrections for multiple comparisons. I am finding a fairly large cluster analyzing 2 groups on sulcal depth. However when I tried FDR or cluster wise correction the results do not seem to survive. As the result is on the region I was predicting I want to make sure there are no other options for correcting for multiple comparisons. I am including a figure of my result to give you an idea of the size of the cluster. Do you have any suggestions for trying alternative ways of correcting? Thank you in advance, Pablo ___ 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 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 -- 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 ___ 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
Re: [Freesurfer] Query about transformations in the recon-all
Hi, Bruce Thanks for your reply. Another question is What is talairach transformation procedure (This computes the affine transform from the orig volume to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script 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 discussing 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 to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach), why I need transform from native space to MNI305; 2. EM (GCA) Registration (Computes transform to align the mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average). What is the GCA atlas? what is the usage of this atlas? 3. CA Register (Computes a nonlinear transform 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) Registration (Affine? 12 dof?); 4. EM Registration, with Skull (Computes transform to align volume mri/nu_noneck.mgz with GCA volume possessing the skull); Is there any detailed documentation in the online manual to introduce these 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 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.
