[Freesurfer] -per-run analysis in native space
Hi Surfers, I want to find a way to analyze subcortical activities in native space and still take advantage of per-run registration. As far as I understand, this is not possible in current preproc-sess. We need one extra step in which we have to map all fmcpr.nii.gz files to subject's orig.mgz. I am trying: mri_vol2vol --mov fmcpr.nii.gz --o fmcpr.native.nii.gz --fstarg orig.mgz --reg register.dof6.dat --no-save-reg --interp trilin in my mind, it is equivalent of what preproc-sess does when we use -mni305 flag (it uses mri_vol2vol to map fmcpr to mni space). Am I right? -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] -per-run analysis in native space
Hi Doug, Selxavg3-sess started without any problem but then I faced the below error. Do you know what is the problem? Global In-Mask Mean = 1316.7 (8.68411) Rescale Target = 100 RescaleFactor = 0.0759477 OLS Residual Pass run 1t= 0.0 Saving rho1 run 2t=144.1 Saving rho1 run 3t=289.9 Saving rho1 run 4t=432.6 Saving rho1 run 5t=580.0 Saving rho1 run 6t=731.8 Saving rho1 run 7t=884.9 Saving rho1 run 8t=1042.3 Saving rho1 run 9t=1194.9 Saving rho1 run 10t=1341.4 Saving rho1 Smoothing ACF /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only: Segmentation fault voxelvolume 1 mm3 Loading mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz Search region is 708874 voxels = 708874.00 mm3 Smoothing input by fwhm=20.00, gstd=8.493218 Segmentation fault (core dumped) ERROR: /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only >> -- ERROR: fast_selxavg3() failed\n On Fri, Mar 27, 2015 at 3:34 PM, Douglas N Greve wrote: > > Yes. Note that that will produce huge files (float images 256^3 by number > of time points). > doug > > > On 03/27/2015 01:50 PM, SHAHIN NASR wrote: > >> Hi Surfers, >> I want to find a way to analyze subcortical activities in native >> space and still take advantage of per-run registration. As far as I >> understand, this is not possible in current preproc-sess. We need one >> extra step in which we have to map all fmcpr.nii.gz files to subject's >> orig.mgz. I am trying: >> >> mri_vol2vol --mov fmcpr.nii.gz --o fmcpr.native.nii.gz --fstarg orig.mgz >> --reg register.dof6.dat --no-save-reg --interp trilin >> >> in my mind, it is equivalent of what preproc-sess does when we use >> -mni305 flag (it uses mri_vol2vol to map fmcpr to mni space). >> >> Am I right? >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> > -- > 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/ > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Measuring the distance relative to a path
Hi Surfers, I need to measure the ''minimum' distance between a cortical vertex and a manually defined path (e.g. V2-V3 border). Is there any command or straightforward way to do that? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] binary noise regressor
Hi Surfers I want to remove the possible effects of a binary noise (electric shock) from the evoked fMRI. To do so, I have generated a regressor file in which all TRs in which electric shock has been applied are marked as 1 and the rest of TRs are 0. I just want to be sure that, this is all I need to do for the regressor! A sample regressor file is attached. It has 98 rows corresponding to 98 TRs that we have in the experiment! Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ShockNUI_Fin Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] binary noise regressor
Hi Doug, Sorry to interrupt you again with this topic. Don't you think, to regress out my unwanted event (eletric shock), I need to convolv this event with the hrf model and then use the outcome as my regressor? Regards On Fri, May 1, 2015 at 12:23 PM, Douglas Greve wrote: > I don't necessarily think the exclude file is a better approach. What you > are doing is probably fine. > doug > > On 5/1/15 12:12 PM, sha...@nmr.mgh.harvard.edu wrote: > >> Hi Doug, >> The reason that we did not use that 'exclusion method' was that, we >> were not sure if the effect of shock is limited to that specific TR. >> Actually, like other stimuli/events, we expected shock effect to appear >> slightly (1-2 TRs) later. In this case, don't you think using a >> regressor is a safer approach? >> To clarify, I am very open to your suggestions if you have a better >> idea or if you still think that exclusion is a better approach. >> >> >> >> >> That will do what you want if you expect the shock to have the same >>> response to each application. Alternatively, you can set up a time point >>> exclude file to exclude those time points. If you use this, then create >>> the file by putting the time in seconds of the time points you want to >>> exclude. >>> doug >>> >>> On 5/1/15 11:45 AM, SHAHIN NASR wrote: >>> >>>> Hi Surfers >>>> I want to remove the possible effects of a binary noise (electric >>>> shock) from the evoked fMRI. To do so, I have generated a regressor >>>> file in which all TRs in which electric shock has been applied are >>>> marked as 1 and the rest of TRs are 0. I just want to be sure that, >>>> this is all I need to do for the regressor! >>>> A sample regressor file is attached. It has 98 rows corresponding >>>> to 98 TRs that we have in the experiment! >>>> >>>> Regards >>>> >>>> -- >>>> Shahin Nasr >>>> >>>> PhD in Cognitive Neuroscience >>>> Martinos Imaging Center, MGH >>>> Harvard Medical School >>>> >>>> >>> >>> >> > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] isxconcat-sess
Hi, Does anyone know what has changed in isxconcat-sess command in nmr-dev-env? Previously I could use it to average different sessions of the same subject. But now I am getting this error: INFO: trgsubject is self, this will fail unless all sessions are the same subject ERROR: cannot find /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] isxconcat-sess
Hi Doug, It works without any error. Thanks a lot On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve wrote: > I just made a fix. Can you try it out and let me know if it works? > > On 05/14/2015 11:38 AM, SHAHIN NASR wrote: > > Hi, > >Does anyone know what has changed in isxconcat-sess command in > > nmr-dev-env? Previously I could use it to average different sessions > > of the same subject. But now I am getting this error: > > > > INFO: trgsubject is self, this will fail unless all sessions are the > > same subject > > ERROR: cannot find > > > /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz > > > > Regards > > -- > > Shahin Nasr > > > > PhD in Cognitive Neuroscience > > Martinos Imaging Center, MGH > > Harvard Medical School > > > > > > ___ > > 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 > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] mris_pmake Error
Hi Surfers, I am using mris_pmake (in nmr-dev-env) to measure the distance between two vertices. Everything is fine as long as I use just one terminal. But, to accelerate my analysis, I have divided my analysis into multiple parts and run each part in one terminal. It means, I may run multiple (tens of) mris_pmake simultaneously (in different terminal or in separate jobs in launchpad). This results this error: *System error: Address already in use* *Fatal error encountered.* * SSocket `Unnamed SSocket_UDP_receive' (id: 0)* * Current function: c_SSocket_UDP_receive::c_SSocket_UDP_receive* * Problem binding to socket 1701* *Error returned from system: Address already in use* *Socket object name: Unnamed SSocket_UDP_receive* *Socket object id: 0* *Socket object type: c_SSocket_UDP_receive* *Socket protocol: Datagram* *Socket ID: 8* *Throwing exception to (this) with code 1* *terminate called after throwing an instance of 'c_SSocket*'* *Abort (core dumped)* How can I avoid this error? I know I can re-do the analysis (when I see this error) and repeat it till I get an answer. But it slows down everything. So, I just want to know how I can avoid it! Regards P.S.: The command that I use it like this: mris_pmake --subject --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:,vertexEnd: --mpmOverlay euclidean -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freesurfer next version
Hi Freesurfer developers, As far as I see, pRF (population receptive field) mapping is not a part of current freesurfer (please correct me if I am wrong). I was wondering if you have any plan to add it to the next/upcoming freesurfer version? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] isxconcat-sess
Hi Surfers and Doug, I was trying to average two scan sessions of the same subject and isxconcat-sess under dev-env failed again. This time I get this message: ERROR: cannot find /autofs/cluster/tootell/pitcairn/1/shahin/FeatureAttention_Color/Subjects2/hron1/bold/Attention_TR3_FHWM0_PR_Ver2.lh/nmask.dat Which is true! this file does not exist. Regards On Thu, May 14, 2015 at 10:39 PM, SHAHIN NASR wrote: > Hi Doug, > It works without any error. > > Thanks a lot > > On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> I just made a fix. Can you try it out and let me know if it works? >> >> On 05/14/2015 11:38 AM, SHAHIN NASR wrote: >> > Hi, >> >Does anyone know what has changed in isxconcat-sess command in >> > nmr-dev-env? Previously I could use it to average different sessions >> > of the same subject. But now I am getting this error: >> > >> > INFO: trgsubject is self, this will fail unless all sessions are the >> > same subject >> > ERROR: cannot find >> > >> /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz >> > >> > Regards >> > -- >> > Shahin Nasr >> > >> > PhD in Cognitive Neuroscience >> > Martinos Imaging Center, MGH >> > Harvard Medical School >> > >> > >> > ___ >> > 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 >> >> >> > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] citation for mris_pmake
Dear Surfer, I want to cite the methods used in mris_pmake command but I can't find it in wikisurfer or the help of this command. Is the method used in this command described in a published paper? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Why don't no-mask flag work?
Hi, I want to test activity outside the brain (around eyes/retina) but when I use "-no-mask" flag in my mkanalysis-sess (to be able to see activity outside brain) as below: mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force -runlistfile RunList -per-run -fsd bold -no-mask I get this error: outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.1mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); >> -- ERROR: fast_selxavg3() failed\n Note: ** I have already used -nomask and -no-subcort-mask in the preproc-sess *** If I remove this flag, everything looks fine except for the fact that all activity outside brain is masked! -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Why don't no-mask flag work?
This time, selxavg3-sess finished without any error but everything outside the brain including eyes are cut (for me i.e. failure). Apparently, no-mask flag is ignored (!). To help you find the problem I copy/paste my commands here: preproc-sess -s Sbj_53/abir/ -fwhm 2 -per-session -fsd bold -no-subcort-mask mkanalysis-sess -analysis RetinaPrj_New -fwhm 2 -paradigm Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -runlistfile RunList -per-session -fsd bold -no-subcort-mask -no-mask selxavg3-sess -s Sbj_53/abir -a RetinaPrj_New I am also attaching the analysis.info If you want to test the files, you can see the subject files in: /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir Note: I did all of these tests from scratch after deleting files from the previous tests. So it can't be due to a remaining file from the previous processes. On Thu, Oct 3, 2013 at 3:47 PM, Douglas N Greve wrote: > > OK, try it like this using the dev env > 1. When you run preproc-sess use -no-subcort-mask but do not spec -nomask > 2. When ruy run mkanalysis-sess use both -no-subcort-mask and -no-mask > > Note that the eyes may get cut off in the mni305 space. You might just > want to keep it in native space. > > doug > > > > > > > On 10/03/2013 03:19 PM, sha...@nmr.mgh.harvard.edu wrote: > >> preproc-sess -s -fwhm 2 -per-run -fsd bold -mni305-1mm -nomask >> -no-subcort-mask >> >> I also tried per-session and mni305-2mm but still did not help. >> I even tried doing it in native space (by not mentioning mni305/fsaverage) >> but did not work either. >> >> >> What was your preproc-sess command? >>> >>> >>> On 10/03/2013 10:29 AM, SHAHIN NASR wrote: >>> >>>> Hi Doug, >>>> Did you have a chance to find the reason for this problem? >>>> >>>> >>>> On Wed, Oct 2, 2013 at 3:20 PM, >>> <mailto:sha...@nmr.mgh.**harvard.edu >> >>>> wrote: >>>> >>>> I still receive the same error message (1mm is now 2mm in the >>>> message). >>>> >>>> outanadir = >>>> /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/** >>>> Sbj_53/abir/bold/RetinaPrj_**nomask2 >>>> Error using MRIread (line 76) >>>> ERROR: cannot determine format of >>>> /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/** >>>> Sbj_53/abir/bold/008/masks/.**mni305.2mm >>>> (MRIread) >>>> >>>> >>>> Error in fast_selxavg3 (line 146) >>>>runmask = MRIread(flac.maskfspec); >>>> >>>> >>>> >>>> > Does the same thing happen if you use the 2mm instead of the 1mm? >>>> > >>>> > On 10/02/2013 02:21 PM, SHAHIN NASR wrote: >>>> >> Hi, >>>> >> I want to test activity outside the brain (around >>>> eyes/retina) but >>>> >> when I use "-no-mask" flag in my mkanalysis-sess (to be able to >>>> see >>>> >> activity outside brain) as below: >>>> >> >>>> >> mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm >>>> >> Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25 >>>> 1.25 >>>> >> -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force >>>> -runlistfile >>>> >> RunList -per-run -fsd bold -no-mask >>>> >> >>>> >> I get this error: >>>> >> >>>> >> outanadir = >>>> >> >>>> /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/** >>>> Sbj_53/abir/bold/RetinaPrj_**nomask >>>> >> Error using MRIread (line 76) >>>> >> ERROR: cannot determine format of >>>> >> >>>> /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/** >>>> Sbj_53/abir/bold/008/masks/.**mni305.1mm >>>> >> (MRIread) >>>> >> >>>> >> >>>> >> Error in fast_selxavg3 (line 146) >>>> >> runmask = MRIread(flac.maskfspec); >>>> >> >> --** >>>> >> ERROR: fast_selxavg3() failed\n >>>> >> >>
[Freesurfer] using multiple functional ROIs in fcseed-config
Hi, I know that we can have multiple segments (segIDs) in fcseed-config. Is there anyway to use multiple ROIs (functionally defined) in fcseed-config? If no, what is the alternative? Is there anyway to average the .dat output files generated by separate fcseed commands? Is it OK to manually average the .dat files? Should we consider anything in this averaging? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] saving in GIFTI .func.gii format
Hi Surfers I have done a surface-based group-averaged mapping and now I need to save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii format. Does mri_glmfit support this output format? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] absolute value of effect size
Hi, I have two related questions. I have two conditions (e.g. C1 and C2) and I want to generate a map that shows all voxels that can differentiate C1 from C2 *irrespective* of whether C1>C2 or C1___ 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] per-run and Native space
I am trying to preproc-sess my data (fwhm 1.5, per-run, native space) with this command preproc-sess -fwhm 1.5 -fsd bold -per-run I expect it to generate fmcpr.sm1.5.nii.gz for each run of my dataset. Although preproc-sess finishes without any error, it only generates fmcpr.nii.gz and when I run selxavg3-sess, it returns an error that > cannot determine format of > test/bold/013/fmcpr.sm1.5 and exits. Would you tell me why those files are not generated? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] selxavg3-sess error
Hi, When I run selxavg3-sess, I face this error: ERROR: cannot find volume matching /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg ERROR: loading nonpar reg /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg -- ERROR: fast_selxavg3() failed\n I repeated the preproc-sess from scratch and it worked fine, finished without any problem and I still get the same error. I even check the registration in this run and it fine. Now I am wondering why do I see this error for this subjects (and why I don't see it for the other subjects)? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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
Hopefully this is the last problem with per-run analysis (in native space) but as far as I see, preproc-sess and selxavg3-sess do not generate /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat Because of that, when I use tksurfer-sess it faces an error: ERROR: cannot find /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat I can use bbregister to register /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/template.nii.gz to the subject's anatomical scan and then use the register.dof.dat file for tksurfer. But is this the correct thing to do? On Wed, Mar 19, 2014 at 11:41 AM, wrote: > YES! Started to work. > > Thanks Doug! > > > use > > -nuisreg mcprextreg 3 > > > > On 03/19/2014 11:34 AM, sha...@nmr.mgh.harvard.edu wrote: > >> I used "-nuisreg mcprextreg" in mkanalysis-sess. Got this error: > >> > >> Error: -nuisreg requires two arguments" > >> > >> > >> > >>> -nuisreg > >>> > >>> On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote: > >>>> Does not accept "-nuis" flag. I changed my mkanalysis-sess to this: > >>>> > >>>> mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 > >>>> -paradigm > >>>> Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -nuis > >>>> mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd bold_Color > >>>> -per-run > >>>> > >>>> and got this error: > >>>> > >>>> ERROR: Flag -nuis unrecognized. > >>>> > >>>> > >>>> > >>>>> I think it is just confused because it expects native to be > >>>>> per-session. > >>>>> One way around this is to just specify -nuis mcprextreg instead of > >>>>> -mcprextreg > >>>>> doug > >>>>> > >>>>> > >>>>> On 03/19/2014 11:15 AM, sha...@nmr.mgh.harvard.edu wrote: > >>>>>> But this is a per-run analysis and preproc-sess is -per-run (in > >>>>>> native > >>>>>> space). I assumed that I have to change my mkanalysis-sess to this: > >>>>>> > >>>>>> mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 > >>>>>> -paradigm > >>>>>> Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 > >>>>>> -mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd > >>>>>> bold_Color > >>>>>> -per-run > >>>>>> > >>>>>> > >>>>>> But using -mcprextreg flag generates an error. Is it a bug? > >>>>>> > >>>>>> > >>>>>>> There is not an mcextreg file there. There is mcprextreg file. I > >>>>>>> think > >>>>>>> you need to run preproc with -per-session to get the mcextreg file > >>>>>>> doug > >>>>>>> > >>>>>>> On 03/18/2014 02:34 PM, SHAHIN NASR wrote: > >>>>>>>> Hi, > >>>>>>>> When I run selxavg3-sess, I face this error: > >>>>>>>> > >>>>>>>> ERROR: cannot find volume matching > >>>>>>>> > /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg > >>>>>>>> ERROR: loading nonpar reg > >>>>>>>> > /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg > >>>>>>>> -- > >>>>>>>> ERROR: fast_selxavg3() failed\n > >>>>>>>> > >>>>>>>> I repeated the preproc-sess from scratch and it worked fine, > >>>>>>>> finished without any problem and I still get the same error. I > >>>>>>>> even > >>>>>>>> check the registration in this run and it fine. > >>>>>>>> > >>>>>>>> Now I am wondering why do I see this error for this subjects > >>>>>>>> (and > >>>>>>>> why I don't see it for the other subjects)? > >>>>>>>> > &
[Freesurfer] mc-bbr
Hi, For a project in which subjects have repeated head movements, I want to register every TR to anatomical scans separately to reduce the effect of head movement as much as possible. When I checked the old posts, I noticed that there has been a code since 2011 ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021691.html) to do this (named mc-bbr). But I am not sure if it is valid any more and not sure how does it works. As far as I see, there is no flag for mc-bbr or something similar to that in preproc-sess. I appreciate if you guide me through it. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] selxavg3-sess problem with -per-run flag
Hi, I used to run my mkanalysis-sess without indicating -per-run or -per-session, assuming that when I have pre-processed my files with -per-run flag then selxavg3-sess will do the same. But when I checked the analysis.info I noticed "PerSession 1" which I think it means system will use per-session preprocessing. So, this time I explicitly used -per-run in my mkanalysis-sess as below: preproc-sess -s -per-run -fwhm 5 -fsd bold -fwhm 5 -surf self rhlh mkanalysis-sess -analysis Reward.rh -surface self rh -native -fwhm 5 -paradigm Conds.par -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 7 -refeventdur .10 -fsd bold -per-run -force This time when I ran selxavg3-sess command I faced this error: ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Reward/Subjects/limi1/bold/004/fmcpr.sm5 (MRIread) Error in flac_customize (line 87) mri = MRIread(fstem,1); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n As I checked my subjects directory I had these files in /bold/004/ directory: fmcpr.nii.gz fmcpr.sm5.self.rh.nii.gz fmcpr.sm5.self.lh.nii.gz Notably, if I drop that -per-run flag from my mkanalysis-sess then system works without any problem. But then I am not sure whether I have processed my data in per-run or per-session mode. Any help will be appreciated Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Comparing HRF undershoots between conditions
Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Fwd: Comparing HRF undershoots between conditions
That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one "particulat time point". What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve wrote: > Hi Shahin, there are several ways that you could do it. The one that > immediately comes to mind is to use an FIR and then test for a difference > at a particular post stimulus time point. > doug > > > > > On 04/10/2013 03:54 PM, SHAHIN NASR wrote: > >> Hi, >> I want to generate a map to show the significant difference between >> HRF undershoot (negative peak of activity) between two conditions >> independent from the positive peak. Is there anyway, to generate this map? >> >> P.S.: Please note that I need a map and not a time course graph. >> >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> > > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Fwd: Comparing HRF undershoots between conditions
Sorry that I keep on asking questions but I want to know if using a model can significantly increase the chance of getting a significant response. As far as I see for the positive peak, when I use a model (e.g. gamma model or spmhrf), I see a more significant response compared to when I use the FIR model. Is it correct? If true, then the same might be correct for the negative peak. P.S.: To be more clear, I am talking about the response maps relative to the baseline. On Apr 10, 2013 6:46 PM, "Douglas N Greve" wrote: > > yes, that is what you want. The only other way that comes to mind is to > model each event type as two event types one delayed relative to the other. > Then model the responseto each as a gamma. If the delay is right, then the > first gamma should model the main positive response and the second gamma > will model the negative response. both will be independent from the other. > > doug > > On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote: > >> I think I figured it out but I want to double check. I am generating >> group-average map for my subjects using isxconcat-sess command which >> generates ces maps for each time frame. I think these maps are what I >> wanted. Right? >> If you still have other solutions that you think may generate more >> reliable results, I am eager to know. For instance, is there anyway to >> fit a model as we do for spmhrf or fslhrf, but just for the negative >> peak? >> >> Regards >> >> That's the problem Doug. I have already generated the FIR model but how >>> can >>> I show the sig MAP for one "particulat time point". What are the other >>> ways? >>> >>> >>> On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve >>> **wrote: >>> >>> Hi Shahin, there are several ways that you could do it. The one that >>>> immediately comes to mind is to use an FIR and then test for a >>>> difference >>>> at a particular post stimulus time point. >>>> doug >>>> >>>> >>>> >>>> >>>> On 04/10/2013 03:54 PM, SHAHIN NASR wrote: >>>> >>>> Hi, >>>>> I want to generate a map to show the significant difference >>>>> between >>>>> HRF undershoot (negative peak of activity) between two conditions >>>>> independent from the positive peak. Is there anyway, to generate this >>>>> map? >>>>> >>>>> P.S.: Please note that I need a map and not a time course graph. >>>>> >>>>> >>>>> -- >>>>> Shahin Nasr >>>>> >>>>> PhD in Cognitive Neuroscience >>>>> Martinos Imaging Center, MGH >>>>> Harvard Medical School >>>>> >>>>> -- >>>> 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<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> >>>> <http://**surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> FileDrop: >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> > >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.*** >>>> *edu/transfer/outgoing/flat/** >>>> greve/ <ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >>>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>> > >>>> >>>> >>>> >>>> >>> -- >>> Shahin Nasr >>> >>> PhD in Cognitive Neuroscience >>> Martinos Imaging Center, MGH >>> Harvard Medical School >>> >>> >>> >>> -- >>> Shahin Nasr >>> >>> PhD in Cognitive Neuroscience >>> Martinos Imaging Center, MGH >>> Harvard Medical School >>> __**_ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <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.
Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions
Hi Doug, Sorry to follow this topic with a delay but we tried to model BOLD signal undershoot with a gamma function and we failed. The problem is, gamma function generates positive values and we can NOT use "inverse gamma function" (or otherfunction similar to that) as a part of mkanalysis-sess (for modeling BOLD signal undershoot). We even used matlab gammafit to estimate parameters and it said that values should be positive otherwise gammafit function fails. Do you have any suggestion? On Wed, Apr 10, 2013 at 6:46 PM, Douglas N Greve wrote: > > yes, that is what you want. The only other way that comes to mind is to > model each event type as two event types one delayed relative to the other. > Then model the responseto each as a gamma. If the delay is right, then the > first gamma should model the main positive response and the second gamma > will model the negative response. both will be independent from the other. > > doug > > > On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote: > >> I think I figured it out but I want to double check. I am generating >> group-average map for my subjects using isxconcat-sess command which >> generates ces maps for each time frame. I think these maps are what I >> wanted. Right? >> If you still have other solutions that you think may generate more >> reliable results, I am eager to know. For instance, is there anyway to >> fit a model as we do for spmhrf or fslhrf, but just for the negative >> peak? >> >> Regards >> >> That's the problem Doug. I have already generated the FIR model but how >>> can >>> I show the sig MAP for one "particulat time point". What are the other >>> ways? >>> >>> >>> On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve >>> **wrote: >>> >>> Hi Shahin, there are several ways that you could do it. The one that >>>> immediately comes to mind is to use an FIR and then test for a >>>> difference >>>> at a particular post stimulus time point. >>>> doug >>>> >>>> >>>> >>>> >>>> On 04/10/2013 03:54 PM, SHAHIN NASR wrote: >>>> >>>> Hi, >>>>> I want to generate a map to show the significant difference >>>>> between >>>>> HRF undershoot (negative peak of activity) between two conditions >>>>> independent from the positive peak. Is there anyway, to generate this >>>>> map? >>>>> >>>>> P.S.: Please note that I need a map and not a time course graph. >>>>> >>>>> >>>>> -- >>>>> Shahin Nasr >>>>> >>>>> PhD in Cognitive Neuroscience >>>>> Martinos Imaging Center, MGH >>>>> Harvard Medical School >>>>> >>>>> -- >>>> 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<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> >>>> <http://**surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> FileDrop: >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> >>>> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> > >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.*** >>>> *edu/transfer/outgoing/flat/** >>>> greve/ <ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >>>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>> > >>>> >>>> >>>> >>>> >>> -- >>> Shahin Nasr >>> >>> PhD in Cognitive Neuroscience >>> Martinos Imaging Center, MGH >>> Harvard Medical School >>> >>> >>> >>> -- >>> Shahin Nasr >>> >>> PhD in Cognitive Neuroscience >>> Martinos Imaging Center, MGH >>> Harvard Medical School >>> __**_ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> &
[Freesurfer] cvs_avg35
Hi, Would you tell me where I can find cvs_avg35 brain template. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] averaging sessions with different TRs
Hi, I was wondering if I can average two scan sessions with different TRs or not. Number of conditions and all other factors are exactly the same between the two sessions. regards ___ 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] Recent paper on FreeSurfer reliability
Please post it on PLoS One homepage. According to the policies of this journal, you are allowed to respond to each paper directly on the same page as the article. You don't need to submit it as a paper and won't go through a review process. On Wed, Jun 20, 2012 at 10:28 AM, Peter J. Molfese < pmolf...@haskins.yale.edu> wrote: > We run things on an Xgrid cluster that is now a mixture of Macs running > Snow Leopard (10.6.8) and Lion (10.7.x). We found the results given from > asegstats2table and aparcstats2table are identical after running 100 > subjects on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1. I also > ran a few subjects on the cluster and on individual computers (not on the > cluster so to speak) and the results are identical. > > Best, > Peter > > > Hi, > > The paper entitled > > “The Effects of FreeSurfer Version, Workstation Type, > and Macintosh Operating System Version on Anatomical > Volume and Cortical Thickness Measurements”, > PLoSONE, Vol 7(6), e38234 (2012) > > may be of interest to all of you. It can be found at: > http://dx.plos.org/10.1371/journal.pone.0038234 > > Cheers, > Ed > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Non rigid registration
Hi, In our functional MRI studies, we co-registration the functional images to anatomical scans (a part of preproc-sess routine in version 5) before measuring the contrasts. But for one of our studies, a reviewer has asked if a “non-rigid image registration” would change results when we are assessing activity within artifact-prone brain areas (e.g. anterior temporal areas). As far as I know, freesurfer registration works fine and even in this study, we have found very strong activity/contrast within anterior tempotal lobe. But I was wondering whether you have tested this possibility or not. If yes, then I appreciate if you can introduce me a reference (published article) to support our answer. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] task-related functional connectivity analyses freesurfer 5.1.0
Hi, I was wondering if we can compare "functional connectivity" between blocks within a run as we do for BOLD signal using freesurfer. Current documentation of freesurfer is for resting state and does not consider conditions that experiment is Blocked Design. Similar question has been asked previous but nobody answered (see the link below) https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] task-related functional connectivity analyses freesurfer 5.1.0
Thanks doug But I am not sure if it was the answer. To be more specific, my subjects did two different tasks within one fmri run. I want to see their functional connectivity during task 1 and task 2 separately. If it was resting state, I didn't need to separate my data and a simple fcseed-config like below was enough: fcseed-config -roi Labels/rh.V1 -fcname mean.R_V1.dat -fsd rest -mean -cfg CFG_Files/mean.R_V1.config But now, I don't know how to modify my fcseed-config to say I have had two conditions (task) within one run and I need to measure the seed for each task separately. On Wed, Oct 24, 2012 at 1:00 PM, Douglas N Greve wrote: > Hi Shahin, you can do seed-based analysis. In principle you can do this > with task data, you just need to adjust your conclusions accordingly. There > is no easy to way to only do the analysis on the resting epochs of a > blocked design, if that is what you mean. > doug > > > On 10/24/2012 12:55 AM, SHAHIN NASR wrote: > >> Hi, >> >>I was wondering if we can compare "functional connectivity" between >> blocks within a run as we do for BOLD signal using freesurfer. Current >> documentation of freesurfer is for resting state and does not consider >> conditions that experiment is Blocked Design. >> >> Similar question has been asked previous but nobody answered (see the >> link below) >> https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2012-** >> June/024394.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html> >> >> Regards >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] High resolution fMRI and resolution of anatomical scans
Hi, We are planning to collect high resolution *functional* MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed *anatomical *scans with 1 mm voxel size. The question is, do we need to re-collect *anatomical* scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] bbregister for MRA
Hi Surfers I want to use bbregister to register my MRA scans to the structural scans. The first attempts by using these parameters came out OK but not perfect: bbregister --s --mov MRA.nii --init-fsl --reg register.dat --bold However, there are obvious problems around frontal areas. I have to admit that one of the reasons for this imperfect registration may be that MRA scans do not cover the whole brain. However, they still cover a large portion of it. I was wondering if there is any argument in bbregister command that may help me improve the quality. It is very fine if it increases the registration time. Regards P.S.: using --t2 in bbregister (instead of --bold) generated the same outcome but --t1 was completely off. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Average myelination within ROI
Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum V1_Stats.txt --accumulate but the numbers don't make any sense. For instance: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 012526182573.4 Seg 110280.4453 0.2922-5.5000 51.56.5000 2 1 1138 764.8 Seg0001 941.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] fieldsign map display
Hi, Have you ran fieldsign-sess after your selxavg3-sess? On Thu, Sep 4, 2014 at 8:35 AM, Francesca Strappini < francescastrapp...@gmail.com> wrote: > Dear all, > > I'm trying to display the fieldsign map. I used standard > rotating-wedge and expanding-ring paradigm, and I followed the steps > described in FsFastIndividualRetinotopy Analysis. > I'm running freesurfer on Ubuntu 14.04. > > Polar angle and eccentricity map look good but I can't properly > display the fieldsign map as an alternation of two colours. I attached > a screen-shot as example. > > Any suggestion? > > Thanks for the help! > Francesca > > The command line is; > tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign > > and that's the output: > > shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy> > tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign > Surface DM lh > Map Surface DM lh > $Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $ > Linux shalim-ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 > 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > Tue Sep 2 17:28:57 IDT 2014 > /usr/local/freesurfer/bin/tksurfer > > list fieldsign > con/map fieldsign > > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz > maplist > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz > mri_concat > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz > --o > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii > ninputs = 1 > Checking inputs > nframestot = 1 > Allocing output > Done allocing > nframes = 1 > Writing to > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii > cd /usr/local/freesurfer/fsfast/MeytalRetinotopy > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects > tksurfer DM lh inflated -overlay > > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii > -label-outline -colscalebarflag 1 -annot aparc -fthresh 0.5 -fmid > 2.2500 -fslope .28571428571428571428 -mask > > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz > -mask-thresh 0.5 -fthresh .01 > > Contrasts > 0 fieldsign > > > setting colscalebarflag to 1 > setting fthresh to 0.5000 > setting fmid to 2.2500 > setting fslope to 0.2857 > mrismaskfile > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz... > setting mrismaskthresh to 0.5000 > setting fthresh to 0.0100 > subject is DM > hemiis lh > surface is inflated > surfer: current subjects dir: /usr/local/freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /usr/local/freesurfer/fsfast/MeytalRetinotopy > checking for nofix files in 'inflated' > Reading image info (/usr/local/freesurfer/subjects/DM) > Reading /usr/local/freesurfer/subjects/DM/mri/orig.mgz > surfer: Reading header info from > /usr/local/freesurfer/subjects/DM/mri/orig.mgz > surfer: vertices=118099, faces=236194 > tkmedit: Trying to open > > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.dat > surfer: Interpreting overlay volume > > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii > as encoded scalar volume. > surfer: curvature read: min=-1.094241 max=1.337460 > reading colortable from annotation file... > colortable with 36 entries read (originally > > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > Found embedded color table in annotation. > 8089 vertices did not have an annotation! > surfer: single buffered window > surfer: tkoInitWindow(DM) > Reading mris mask > > /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz > surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl > Reading /usr/local/freesurfer/tktools/tkm_common.tcl > Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl > Reading /usr/local/freesurfer/tktools/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > % ^CKilled > Area degli allegati > Visualizza anteprima allegato fieldsign_map.tiff > Fai clic qui per rispondere o inoltrare il messaggio > 7,02 GB (46%) di 15 GB utilizzati > Gestisci > Ultima attività dell'account: 2 minuti fa > Dettagli > > _
Re: [Freesurfer] bbregister for MRA
Hi Doug, Sorry for interrupting you again with this topic but recently we changed couple of parameters in our MRA to increase our chance or detecting veins. The problem is that, bbregister can not register the MRA volume to T1 scans anymore. As an example, here you can see the old version of our MRA and how good it was when we used T1+pial registeration: tkregister2 --mov /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/001_nu.nii --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/register_t1_pial.dat --surf And here, you can see the new one: tkregister2 --mov /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_TOF_2D_500_fa70_cor/018/001_nu.nii --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_TOF_2D_500_fa70_cor/018/register_t1_pial.dat --surf Now I have two questions: 1) Is there anyway to improve this registration? 2) Since I collect both MRA types in one session, can I use the good volume (or registrations) to help registering the second volume? I actually used --init-reg but it did not help. Regards On Wed, Aug 20, 2014 at 5:06 PM, Douglas N Greve wrote: > > Using --t2 and --bold will always give identical results. If there is not > much G/W contrast in the MRA (and there probably isn't), then you can try > using the pial surface instead (maybe more GM/CSF contrast). Use --surf > pial --t1. Use --t1 here because the GM will probably be brighter than CSF. > > doug > > > > On 08/20/2014 04:54 PM, SHAHIN NASR wrote: > >> Hi Surfers >> I want to use bbregister to register my MRA scans to the structural >> scans. The first attempts by using these parameters came out OK but not >> perfect: >> >> bbregister --s --mov MRA.nii --init-fsl --reg register.dat >> --bold >> >> However, there are obvious problems around frontal areas. >> >> I have to admit that one of the reasons for this imperfect registration >> may be that MRA scans do not cover the whole brain. However, they still >> cover a large portion of it. I was wondering if there is any argument in >> bbregister command that may help me improve the quality. It is very fine >> if it increases the registration time. >> >> Regards >> >> P.S.: using --t2 in bbregister (instead of --bold) generated the same >> outcome but --t1 was completely off. >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> > -- > 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/ > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] bbregister for MRA
For the record, I applied two changes: 1) I used my AAScout scan as --int and it worked. 2) As you suggested I also used --t2 rather than --t1 this time and it also helped. Combination of these two changes worked very well. Thanks On Tue, Sep 30, 2014 at 1:11 PM, Douglas N Greve wrote: > > A couple of suggestions ... > > It looks like the new sequence is T2 weighted, so you can try using --t2 > with the white surface > > It may be that the fsl is not initializing the BBR registration properly. > Try using spm (which may still fail because it is partial brain coverage). > Do you have a whole-brain volume that was acquired during the same session > as the MRA? If not, you should start collecting this. If so, then use that > as an intermediate (--int). It will use fsl/spm to register the whole-brain > to the anatomical using standard volume reg, then transfer that > registration to the partial FoV assuming that the whole and partial share a > scanner space (which they will if acquired at the same time). The > intermediate can be anything, eg, fMRI, anatomical, B0 map, low-b DTI > volume. > > doug > > > > > > > On 09/30/2014 12:41 PM, SHAHIN NASR wrote: > >> Hi Doug, >> Sorry for interrupting you again with this topic but recently we >> changed couple of parameters in our MRA to increase our chance or detecting >> veins. The problem is that, bbregister can not register the MRA volume to >> T1 scans anymore. >> >> As an example, here you can see the old version of our MRA and how >> good it was when we used T1+pial registeration: >> >> tkregister2 --mov /cluster/tootell/pitcairn/1/ >> shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/001_nu.nii >> --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/ >> auil_2/MRA_500_pre_contrast/010/register_t1_pial.dat --surf >> >> And here, you can see the new one: >> >> tkregister2 --mov /cluster/tootell/pitcairn/1/ >> shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_TOF_2D_500_fa70_cor/018/001_nu.nii >> --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/ >> auil_2/MRA_TOF_2D_500_fa70_cor/018/register_t1_pial.dat --surf >> >> Now I have two questions: >> 1) Is there anyway to improve this registration? >> 2) Since I collect both MRA types in one session, can I use the good >> volume (or registrations) to help registering the second volume? I >> actually used --init-reg but it did not help. >> >> Regards >> >> On Wed, Aug 20, 2014 at 5:06 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> Using --t2 and --bold will always give identical results. If there >> is not much G/W contrast in the MRA (and there probably isn't), >> then you can try using the pial surface instead (maybe more GM/CSF >> contrast). Use --surf pial --t1. Use --t1 here because the GM will >> probably be brighter than CSF. >> >> doug >> >> >> >> On 08/20/2014 04:54 PM, SHAHIN NASR wrote: >> >> Hi Surfers >> I want to use bbregister to register my MRA scans to the >> structural scans. The first attempts by using these >> parameters came out OK but not perfect: >> >> bbregister --s --mov MRA.nii --init-fsl --reg >> register.dat --bold >> >> However, there are obvious problems around frontal areas. >> >> I have to admit that one of the reasons for this imperfect >> registration may be that MRA scans do not cover the whole >> brain. However, they still cover a large portion of it. I was >> wondering if there is any argument in bbregister command that >> may help me improve the quality. It is very fine if it >> increases the registration time. >> >> Regards >> >> P.S.: using --t2 in bbregister (instead of --bold) generated >> the same outcome but --t1 was completely off. >> -- Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> File
Re: [Freesurfer] FIR analysis on regions of interest...
Hi Joe, I assume that you have already 1) defined your FIR function (mkanalysis-sess) and applied it (selxavg3-sess). I also assume that you have already defined your ROIs (funcroi-config) and applied them (funcroi-sess). Up to this point, everything is more or less easy. Now, you want to know how to get your time course! You have to use funcroi-table-sess command multiple times! For FIR analysis, you have to add '-frame X' to your funcroi-table-sess command with X referring to the point in your time course (use funcroi-table-sess --help for more help). You have to repeat this command for each TR in your time course. For example if you have 10 TR, then you have to repeat it 10 times with '-frame 0' to '-frame 9'. Please note that, you have to save the results in 10 different files and then read them later somehow (I use matlab for that) and combine them to make your time course. Let me know if you faced a problem Good Luck On Tue, Oct 14, 2014 at 10:24 PM, Douglas Greve wrote: > > It is still possible but not quite as easy. You have to create a > contrast for each tap in the FIR, then run funcroi for each tap. > doug > > > On 10/14/14 7:02 PM, Joseph Andreano wrote: > > Hi All, > > > > I'm trying to extract signal from an ROI in an analysis that I specified > > as FIR. Using funcroi-config and funcroi-table-sess, I'm able to produce > > an output file that gives me a single value for each participant. What > > I'm trying to do is to get a value for each TR in the time window I > > specified so that I can generate a time course for that ROI. I know that > > this was possible with the older analysis tools in the older version of > > freesurfer (ie func2roi-sess and roisummary-sess, but the newer tools are > > just giving me a single (presumably averaged) value. Does anyone know > how > > I can get a timecourse for my ROI? > > > > Thanks, > > Joe > > > > > > _ > > > > Joseph M. Andreano, PhD > > Postdoctoral Researcher > > Interdisciplinary Affective > > Science Laboratory > > Massachusetts General Hospital > > _ > > ___ > > 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 > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] registration problem
Hi, For one of my subjects, I have noticed a misalignment between sig.nii and orig.mgz when I try to show the sig map using either tkmedit (as below): cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45 or tkmedit-sess: cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Subjects tkmedit auil_anat orig.mgz -overlay auil2/bold/OriExp_TR3_1p5mm_PR/ANG_90_45/abs_sig.nii.gz -reg auil2/bold/register.dof6.dat~ I checked the registration file for this subjects and I don't see this problem there. tkregister2 --reg ../Subjects/auil2/bold/register.dof6.dat~ --mov ../Subjects/auil2/bold/template.nii.gz --surf I also checked the brain.mask and it covers the whole brain and looks fine to me. I also checked my other subjects and their results are fine. Do you have any idea why this is happening? P.S.: I process my data in in nmr-dev-env but I have also checked the above lines in nmr-stable53-env and problem is still there. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Problem with fcseed-config and fcseed-sess
Hi, I have faced a problem using ROI-based, fcseed-config and fcseed-sess I used either: fcseed-config -roi /cluster/tootell/pitcairn/1/shahin/good_subjects_anat/atou_anat/label/rh.V1.label -fcname mean.R_V1.dat -fsd bold -mean -cfg mean.R_V1.config OR: fcseed-config -roi /cluster/tootell/pitcairn/1/shahin/good_subjects_anat/fsaverage/label/rh.V1.label -fcname mean.R_V1.dat -fsd bold -mean -cfg mean.R_V1.config to generated the mean.R_V1.config file for right V1 area (ROI for V1 is generated automatically and I have not changed it). Then I use below command to generate mean.R_V1.dat for the session of interest (e.g. atou) fcseed-sess -s atou -cfg mean.R_V1.config -make-mask but I just get a "if: Expression Syntax." message and the expected dat file is not generated. Do you have any idea what is wrong? Any help will be highly appreciated. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Partial brain scanning and registeration
Hi I want to know if there is any limit for the automatic registration of functional scans on structural ones when we are scanning activity just in a specific part of the brain (e.g. occipital cortex). ___ 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 isxconcat for partial correlation coefficient map
Hi, Would you tell me how can I use isxconcat-sess to calculate group averaged "partial correlation coefficient map"? I have already generated pcc.nii files for each individual subject. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] funcroi-table-sess with multiple contrasts
Hi, Is there anyway to print multiple contrasts in one output file using funcroi-table-sess command? -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] problem with generating cesvar.nii
Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. > mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: > mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: "Error: MRInormWeights: values less than or eq to 0" which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] problem with generating cesvar.nii
Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve wrote: > Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. > What you are trying to get is the expected variance of your difference > between the ces files (as a variance, it must be positive). To get this you > need > > cesvardiff = (cesvar1+cesvar2)/(2^2) > > The 2^2 is the number of inputs (2) squared. > > doug > > > SHAHIN NASR wrote: > >> Hi, >> >> I have generated two different functional connectivity maps for two >> different ROI-based seeds. These maps are based on group-average of the same >> subjects (generated by using separate isxconcat-sess commands ), and now I >> want to see the difference map. To do so, I used mris_calc as below. >> > mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub >> map2/rh.ces.nii >> >> Also, to generate the rh.cesvar.nii file I used this command: >> > mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub >> map2/rh.cesvar.nii >> >> But then when I used the glmfit with WLS option as below: >> >> > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask >> ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf >> fsaverage rh --wls rh.cesvar.nii >> >> I faced an error saying: "Error: MRInormWeights: values less than or eq >> to 0" which I assumed is related to an error in rh.cesvar.nii file (am I >> right?). Would you tell me how can I fix this problem? >> >> P.S.: please note that sequence of subjects and all MRI parameters are >> exactly the same between the two maps. >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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<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. > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] problem with generating cesvar.nii
Do you suggest using random-effect model? Is there any problem with using a fix-effect model (other than the fact that by using this model we can not predict response of subjects outside our population)? On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve wrote: > > It should be roughly the sum of the dofs of the individual subjects. Why > are you using a fixed-effects model? > doug > > SHAHIN NASR wrote: > >> Thanks Doug. Just one related question. Should I also generate a new >> ffxdof.dat file for this map? I assumed that ffxdof depends on the number of >> subjects (session) and since number of subjects (sessions) is the same >> between the two groups then I can use those values, generated by >> isxconcat-sess for either map1 or map2. Right? >> >> >> >> On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >>Hi Shahin, it is not as simple as doing a subtraction of the >>cesvar files. What you are trying to get is the expected variance >>of your difference between the ces files (as a variance, it must >>be positive). To get this you need >> >>cesvardiff = (cesvar1+cesvar2)/(2^2) >> >>The 2^2 is the number of inputs (2) squared. >> >>doug >> >> >>SHAHIN NASR wrote: >> >>Hi, >> >> I have generated two different functional connectivity maps >>for two different ROI-based seeds. These maps are based on >>group-average of the same subjects (generated by using >>separate isxconcat-sess commands ), and now I want to see the >>difference map. To do so, I used mris_calc as below. >>> mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub >> map2/rh.ces.nii >> >>Also, to generate the rh.cesvar.nii file I used this command: >> > mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii >> sub map2/rh.cesvar.nii >> >>But then when I used the glmfit with WLS option as below: >> >>> mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls >>--nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii >>--ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii >> >> I faced an error saying: "Error: MRInormWeights: values less >>than or eq to 0" which I assumed is related to an error in >>rh.cesvar.nii file (am I right?). Would you tell me how can I >>fix this problem? >> >>P.S.: please note that sequence of subjects and all MRI >>parameters are exactly the same between the two maps. >> >>-- Shahin Nasr >> >>PhD in Cognitive Neuroscience >>Martinos Imaging Center, MGH >>Harvard Medical School >> >> >>-- Douglas N. Greve, Ph.D. >>MGH-NMR Center >>gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu >> > >>Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> >>Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >>FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> >> >>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<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. >> >> >> >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu >
[Freesurfer] Event-Related design and jitter in stimulus onset
Hi Surfers, It is my first experience with Event-related paradigms. In my experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum variable delay between trials to be able to analyze data without any confound. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Event-Related design and jitter in stimulus onset
Thanks Doug. In my experiment, each trial (event) consists of 1 sec stimulus presentation and 5 sec blank interval (TR=2). I have also added a condition with just blank presentation which will be repeated as much as other events. I have used optseq2 commands to generate the trial sequence. But I faced two problem/questions: 1) Using this command, I expected to see a Null event (other than my blank condition) with variable length (irrespective of TR) between other trials. But to my surprise, length of the Null event was always a multiplication of TR. Is that correct? 2) Also, for "psdmin psdmax" I wasn't sure if they are number of TRs or number of seconds and what is a safe window length when my stimuli are very simple visual objects (and no cognitive task). Once again, thanks for your help. On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve wrote: > Hi Shahin, there are several ways to answer this question. If you are > going to analyze assuming a shape to the HRF, then the actual delay between > stimuli is technically not important (though 4s will be good to avoid > attenuation in the following stimulus). If you're using an FIR model of the > HRF (no assumed shape), then I usually advise that you have, in total, as > much time spent on fixation (or whatever your null stimulus is) as you have > for any other stimulus. You can use optseq to compute the actual schedule. > doug > > > SHAHIN NASR wrote: > >> Hi Surfers, >> >> It is my first experience with Event-related paradigms. In my >> experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum >> variable delay between trials to be able to analyze data without any >> confound. >> >> Regards >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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<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. > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Selxavg3-sess Out of Memory - What are the options?
Hi, I am running selxavg3-sess under freesurfer 4.5 and I faced "out of memory error" as it started "computing whitening matrices". Since they are monkey datasets, runs were relatively long (12 runs each 16 min; TR=1.4). I want to know what options do I have here? Please note that, when I applied this command to 3 runs rather than all 12 runs (by making a runlist), I didn't face this error. P.S.: I can not use version 5.1 because we don't have structural scan for this monkey and we just want to check the functional scans without any registration. I assume it is not possible in version 5. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Per-run registration in monkey fmri
Hi In monkey fmri, we usually have to do the functional-anatomical registration manually since bbregister doesn't work very well. It was easy in version 4.5 since we usually used just one run for registration. In version 5.1 we can use per-run option to improve registration but I am wondering how can we use it in monkey fmri? Should we register each run separately? Then how can we combine those individual registration files to generate the final registration file. ___ 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.
