[Freesurfer] Tracula - Bedpostx - missing output
Hi, I am running bedpostx within Freesurfer Tracula with default settings. I got the following error message: Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. Below the individual slice folder I have the followings: dyads1.nii.gz, logfile, mean_f2samples.nii.gz, th2samples.nii.gz, dyads2.nii.gz, mean_S0samples.nii.gz ph1samples.nii.gz, f1samples.nii.gz, mean_dsamples.nii.gz, ph2samples.nii.gz, f2samples.nii.gz , mean_f1samples.nii.gz, th1samples.nii.gz. But I miss all the 3 and 4D volume below bedpostx dir. Is it possible that only the postprocessing step went wrong? Thanks for your help. Best regards, Judit Haasz, MD Neuroinformatics and Image Analysis Group, UiB, Norway ___ 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] Tracula - Bedpostx - missing output
Hi Judit - Hard to tell what could've gone wrong but you can try running the postprocessing yourself as follows: bedpostx_postproc.sh /path/to/subject/dmri Hope this helps, a.y On Thu, 8 Sep 2011, Judit Haasz wrote: Hi, I am running bedpostx within Freesurfer Tracula with default settings. I got the following error message: Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. Below the individual slice folder I have the followings: dyads1.nii.gz, logfile, mean_f2samples.nii.gz, th2samples.nii.gz, dyads2.nii.gz, mean_S0samples.nii.gz ph1samples.nii.gz, f1samples.nii.gz, mean_dsamples.nii.gz, ph2samples.nii.gz, f2samples.nii.gz , mean_f1samples.nii.gz, th1samples.nii.gz. But I miss all the 3 and 4D volume below bedpostx dir. Is it possible that only the postprocessing step went wrong? Thanks for your help. Best regards, Judit Haasz, MD Neuroinformatics and Image Analysis Group, UiB, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_convert: orientation issue
Hello, I am using mri_convert to convert dicom image into analyze format using: mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.img The problem is: The hdr.hist.orient in the output file is set to 0, but the pixels in the analyze image are saggital. Does anybody have any suggestions as to what could be wrong? Regards Mohana Ramaratnam DIAGNOSTICS: mri_info on the dicom reports: Orientation : PIL Primary Slice Direction: sagittal and that on the analyze image reports: Orientation : LAS Primary Slice Direction: axial OUTPUT of mri_convert: INFO: Scanning for Series Number 4 INFO: found 176 files in series INFO: loading series header info. INFO: sorting. RunNo = 3 INFO: (256 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix - 0.998 0.038 -0.051 -2.542; -0.051 0.954 -0.294 -15.875; 0.038 0.296 0.954 -2.910; 0.000 0.000 0.000 1.000; FileNameFILE_NAME_HERE Identification NumarisVersyngo MR B17 ScannerModel TrioTim PatientName 65433 Date and time StudyDate 20110708 StudyTime 110252.125000 SeriesTime111446.078000 AcqTime 110635.592500 Acquisition parameters PulseSeq tfl3d1_ns Protocol t1_mpr_1mm_p2_pos50 PhEncDir ROW EchoNo1 FlipAngle 8 EchoTime 3.16 InversionTime 1000 RepetitionTime2400 PhEncFOV 256 ReadoutFOV256 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows256 NImageCols256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos104.6950 154.3827 112.3121 VolRes 1. 1. 1. VolDim256 256 176 Vc -0.0493 -0.9976 0.0480 Vr -0.0403 -0.0460 -0.9981 Vs -0.9980 0.0511 0.0379 VolCenter 5.4129 25.2910 -5.9690 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 i_ras = (-0.0492738, -0.997631, 0.0480037) j_ras = (-0.0402601, -0.0460391, -0.998128) k_ras = (-0.997974, 0.0511142, 0.0378956) writing to 110708_TC33875.img... Analyze Output Matrix -0.049 -0.040 -0.998 105.782; -0.998 -0.046 0.051 155.375; 0.048 -0.998 0.038 113.224; 0.000 0.000 0.000 1.000; No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for FILE_NAME_HERE are: x_r = -0.0493, y_r = -0.0403, z_r = -0.9980, c_r = 5.4129 x_a = -0.9976, y_a = -0.0460, z_a = 0.0511, c_a =25.2910 x_s = 0.0480, y_s = -0.9981, z_s = 0.0379, c_s =-5.9690 INFO: set hdr.hist.orient to 'transverse unflipped' ___ 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] mri_convert: orientation issue
I have no idea. That's pretty old code that we are not really maintaining anymore. Why are you using analyze? doug Mohana Ramaratnam wrote: Hello, I am using mri_convert to convert dicom image into analyze format using: mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.img The problem is: The hdr.hist.orient in the output file is set to 0, but the pixels in the analyze image are saggital. Does anybody have any suggestions as to what could be wrong? Regards Mohana Ramaratnam DIAGNOSTICS: mri_info on the dicom reports: Orientation : PIL Primary Slice Direction: sagittal and that on the analyze image reports: Orientation : LAS Primary Slice Direction: axial OUTPUT of mri_convert: INFO: Scanning for Series Number 4 INFO: found 176 files in series INFO: loading series header info. INFO: sorting. RunNo = 3 INFO: (256 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix - 0.998 0.038 -0.051 -2.542; -0.051 0.954 -0.294 -15.875; 0.038 0.296 0.954 -2.910; 0.000 0.000 0.000 1.000; FileNameFILE_NAME_HERE Identification NumarisVersyngo MR B17 ScannerModel TrioTim PatientName 65433 Date and time StudyDate 20110708 StudyTime 110252.125000 SeriesTime111446.078000 AcqTime 110635.592500 Acquisition parameters PulseSeq tfl3d1_ns Protocol t1_mpr_1mm_p2_pos50 PhEncDir ROW EchoNo1 FlipAngle 8 EchoTime 3.16 InversionTime 1000 RepetitionTime2400 PhEncFOV 256 ReadoutFOV256 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows256 NImageCols256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos104.6950 154.3827 112.3121 VolRes 1. 1. 1. VolDim256 256 176 Vc -0.0493 -0.9976 0.0480 Vr -0.0403 -0.0460 -0.9981 Vs -0.9980 0.0511 0.0379 VolCenter 5.4129 25.2910 -5.9690 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 i_ras = (-0.0492738, -0.997631, 0.0480037) j_ras = (-0.0402601, -0.0460391, -0.998128) k_ras = (-0.997974, 0.0511142, 0.0378956) writing to 110708_TC33875.img... Analyze Output Matrix -0.049 -0.040 -0.998 105.782; -0.998 -0.046 0.051 155.375; 0.048 -0.998 0.038 113.224; 0.000 0.000 0.000 1.000; No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for FILE_NAME_HERE are: x_r = -0.0493, y_r = -0.0403, z_r = -0.9980, c_r = 5.4129 x_a = -0.9976, y_a = -0.0460, z_a = 0.0511, c_a =25.2910 x_s = 0.0480, y_s = -0.9981, z_s = 0.0379, c_s =-5.9690 INFO: set hdr.hist.orient to 'transverse unflipped' ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] FS-FAST modeling question
Ben Deen wrote: Hi, I have an update to this query. I tried using mkanalysis-sess instead of the .new version, and now I do seem to be able to get rid of intensity normalization and prewhitening (or at least, adding these flags now has an effect on betas/t-stats, and in the expected directions). The code I'm using is mkanalysis-sess -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -no-inorm -nowhiten -noautostimdur # mkcontrast stuff here... selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 However, I have a few remaining questions about the results. 1) When I look at the regressors used in the analysis, they have a surprisingly large magnitude -- the HRF peaks at a value of ~20. Is there any way to alter the analysis such that these peaks are comparable to the values used in FSL/SPM, which is around .8, so that beta values will be directly comparable across analyses? If not, I can just scale the betas by the relevant factor, but it would be nice if this were possible. No not really. The 5.1 version controls this better (but you still can't set a scaling parameter). You can play with the -TER parameter. By default it is set to .01, I think, which causes the amplitude to be very large. If your events appear on the TR, then try setting it to the TR. 2) When I compare the results of this analysis to results obtained with FSL or SPM, I find that the spatial pattern of beta/t-stats is very similar, but the t-stats have a noticeably reduced magnitude across the brain. Is there anything that may differ about FS-FAST's implementation of the GLM, such that t-stats would differ? You might try turning off the whitening (--no-whiten I think). 3) I saw in a ppt presentation on FS-FAST that the option -hpf can be used to add a highpass temporal filter to the model. However, when I use this option with mkanalysis-new, the script says that the flag isn't recognized. Is there another way to add such a filter? It's in the 5.X version. doug Thanks in advance for any help. Cheers, Ben On Mon, Sep 5, 2011 at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 1 Date: Sun, 4 Sep 2011 13:15:51 -0400 From: Benjamin Matthew Deen bd...@mit.edu Subject: [Freesurfer] FS-FAST modeling question To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: d0755b22ea5ed64c941ed568237aec8d1764dcc...@expo11.exchange.mit.edu Content-Type: text/plain; charset=us-ascii Hi, I'm trying to run a model in fs-fast using no intensity normalization and no autocorrelation correction, for the purpose of comparing results with other software packages, and comparing results with/without autocorrelation correction. However, I haven't been able to get this to work so far. I've tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these don't seem to have any effect on the results: noinorm doesn't change the beta values, and nowhiten doesn't change either betas or t-stats, at all. The commands I'm using are: mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm -nowhiten mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1 -c 2 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2 -c 1 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1 -a 2 -c 0 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 -a 0 -c 1 -c 2 selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 Any idea what might be going wrong, or how I can get this to work? Thanks, Ben ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] FS-FAST modeling question
Hi Doug, Thanks for your response. The comments below all regard question #2, is this is the only one that still concerns me. I actually was using the nowhiten flag in the last analysis I described, which was run in version 4.5. From looking at the ces, cesvar, and t images in the contrast directories, I am finding that the value of t is not equal to ces/sqrt(cesvar), so I believe that this analysis is producing erroneous t-stats. I've checked results from analyses run by other members of my lab, for which the entire processing stream was performed in fs-fast (my data was preprocessed in FSL and then modeled with FS-FAST, in case that matters). Their results do not have this discrepancy, indicating that something is wrong with the specific commands I'm using. Also, when I model the data using version 5.1, I also do not see this discrepancy. Anyway, this is no longer an issue for me as I'm fine using version 5.1 for the analyses, but I thought this should be mentioned, in case in reflects a bug in the older modeling scripts. best, Ben On Thu, Sep 8, 2011 at 2:29 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Ben Deen wrote: Hi, I have an update to this query. I tried using mkanalysis-sess instead of the .new version, and now I do seem to be able to get rid of intensity normalization and prewhitening (or at least, adding these flags now has an effect on betas/t-stats, and in the expected directions). The code I'm using is mkanalysis-sess -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -no-inorm -nowhiten -noautostimdur # mkcontrast stuff here... selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 However, I have a few remaining questions about the results. 1) When I look at the regressors used in the analysis, they have a surprisingly large magnitude -- the HRF peaks at a value of ~20. Is there any way to alter the analysis such that these peaks are comparable to the values used in FSL/SPM, which is around .8, so that beta values will be directly comparable across analyses? If not, I can just scale the betas by the relevant factor, but it would be nice if this were possible. No not really. The 5.1 version controls this better (but you still can't set a scaling parameter). You can play with the -TER parameter. By default it is set to .01, I think, which causes the amplitude to be very large. If your events appear on the TR, then try setting it to the TR. 2) When I compare the results of this analysis to results obtained with FSL or SPM, I find that the spatial pattern of beta/t-stats is very similar, but the t-stats have a noticeably reduced magnitude across the brain. Is there anything that may differ about FS-FAST's implementation of the GLM, such that t-stats would differ? You might try turning off the whitening (--no-whiten I think). 3) I saw in a ppt presentation on FS-FAST that the option -hpf can be used to add a highpass temporal filter to the model. However, when I use this option with mkanalysis-new, the script says that the flag isn't recognized. Is there another way to add such a filter? It's in the 5.X version. doug Thanks in advance for any help. Cheers, Ben On Mon, Sep 5, 2011 at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 1 Date: Sun, 4 Sep 2011 13:15:51 -0400 From: Benjamin Matthew Deen bd...@mit.edu Subject: [Freesurfer] FS-FAST modeling question To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: d0755b22ea5ed64c941ed568237aec8d1764dcc...@expo11.exchange.mit.edu Content-Type: text/plain; charset=us-ascii Hi, I'm trying to run a model in fs-fast using no intensity normalization and no autocorrelation correction, for the purpose of comparing results with other software packages, and comparing results with/without autocorrelation correction. However, I haven't been able to get this to work so far. I've tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these don't seem to have any effect on the results: noinorm doesn't change the beta values, and nowhiten doesn't change either betas or t-stats, at all. The commands I'm using are: mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm -nowhiten mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1 -c 2 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2 -c 1 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1 -a 2 -c 0 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 -a 0 -c 1 -c 2 selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 Any idea what might be going wrong, or how I can get this to work? Thanks, Ben
Re: [Freesurfer] FS-FAST modeling question
So, which version did you find that ces/sqrt(cesvar) did not equal t? doug Ben Deen wrote: Hi Doug, Thanks for your response. The comments below all regard question #2, is this is the only one that still concerns me. I actually was using the nowhiten flag in the last analysis I described, which was run in version 4.5. From looking at the ces, cesvar, and t images in the contrast directories, I am finding that the value of t is not equal to ces/sqrt(cesvar), so I believe that this analysis is producing erroneous t-stats. I've checked results from analyses run by other members of my lab, for which the entire processing stream was performed in fs-fast (my data was preprocessed in FSL and then modeled with FS-FAST, in case that matters). Their results do not have this discrepancy, indicating that something is wrong with the specific commands I'm using. Also, when I model the data using version 5.1, I also do not see this discrepancy. Anyway, this is no longer an issue for me as I'm fine using version 5.1 for the analyses, but I thought this should be mentioned, in case in reflects a bug in the older modeling scripts. best, Ben On Thu, Sep 8, 2011 at 2:29 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Ben Deen wrote: Hi, I have an update to this query. I tried using mkanalysis-sess instead of the .new version, and now I do seem to be able to get rid of intensity normalization and prewhitening (or at least, adding these flags now has an effect on betas/t-stats, and in the expected directions). The code I'm using is mkanalysis-sess -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -no-inorm -nowhiten -noautostimdur # mkcontrast stuff here... selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 However, I have a few remaining questions about the results. 1) When I look at the regressors used in the analysis, they have a surprisingly large magnitude -- the HRF peaks at a value of ~20. Is there any way to alter the analysis such that these peaks are comparable to the values used in FSL/SPM, which is around .8, so that beta values will be directly comparable across analyses? If not, I can just scale the betas by the relevant factor, but it would be nice if this were possible. No not really. The 5.1 version controls this better (but you still can't set a scaling parameter). You can play with the -TER parameter. By default it is set to .01, I think, which causes the amplitude to be very large. If your events appear on the TR, then try setting it to the TR. 2) When I compare the results of this analysis to results obtained with FSL or SPM, I find that the spatial pattern of beta/t-stats is very similar, but the t-stats have a noticeably reduced magnitude across the brain. Is there anything that may differ about FS-FAST's implementation of the GLM, such that t-stats would differ? You might try turning off the whitening (--no-whiten I think). 3) I saw in a ppt presentation on FS-FAST that the option -hpf can be used to add a highpass temporal filter to the model. However, when I use this option with mkanalysis-new, the script says that the flag isn't recognized. Is there another way to add such a filter? It's in the 5.X version. doug Thanks in advance for any help. Cheers, Ben On Mon, Sep 5, 2011 at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 1 Date: Sun, 4 Sep 2011 13:15:51 -0400 From: Benjamin Matthew Deen bd...@mit.edu Subject: [Freesurfer] FS-FAST modeling question To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: d0755b22ea5ed64c941ed568237aec8d1764dcc...@expo11.exchange.mit.edu Content-Type: text/plain; charset=us-ascii Hi, I'm trying to run a model in fs-fast using no intensity normalization and no autocorrelation correction, for the purpose of comparing results with other software packages, and comparing results with/without autocorrelation correction. However, I haven't been able to get this to work so far. I've tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these don't seem to have any effect on the results: noinorm doesn't change the beta values, and nowhiten doesn't change either betas or t-stats, at all. The commands I'm using are: mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm -nowhiten mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1 -c 2 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2 -c 1 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1 -a 2 -c 0 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 -a 0 -c 1 -c 2 selxavg3-sess -sf sessid
Re: [Freesurfer] FS-FAST modeling question
4.5, but only for my results, not others from my lab. On Thu, Sep 8, 2011 at 3:37 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: So, which version did you find that ces/sqrt(cesvar) did not equal t? doug Ben Deen wrote: Hi Doug, Thanks for your response. The comments below all regard question #2, is this is the only one that still concerns me. I actually was using the nowhiten flag in the last analysis I described, which was run in version 4.5. From looking at the ces, cesvar, and t images in the contrast directories, I am finding that the value of t is not equal to ces/sqrt(cesvar), so I believe that this analysis is producing erroneous t-stats. I've checked results from analyses run by other members of my lab, for which the entire processing stream was performed in fs-fast (my data was preprocessed in FSL and then modeled with FS-FAST, in case that matters). Their results do not have this discrepancy, indicating that something is wrong with the specific commands I'm using. Also, when I model the data using version 5.1, I also do not see this discrepancy. Anyway, this is no longer an issue for me as I'm fine using version 5.1 for the analyses, but I thought this should be mentioned, in case in reflects a bug in the older modeling scripts. best, Ben On Thu, Sep 8, 2011 at 2:29 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Ben Deen wrote: Hi, I have an update to this query. I tried using mkanalysis-sess instead of the .new version, and now I do seem to be able to get rid of intensity normalization and prewhitening (or at least, adding these flags now has an effect on betas/t-stats, and in the expected directions). The code I'm using is mkanalysis-sess -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -no-inorm -nowhiten -noautostimdur # mkcontrast stuff here... selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 However, I have a few remaining questions about the results. 1) When I look at the regressors used in the analysis, they have a surprisingly large magnitude -- the HRF peaks at a value of ~20. Is there any way to alter the analysis such that these peaks are comparable to the values used in FSL/SPM, which is around .8, so that beta values will be directly comparable across analyses? If not, I can just scale the betas by the relevant factor, but it would be nice if this were possible. No not really. The 5.1 version controls this better (but you still can't set a scaling parameter). You can play with the -TER parameter. By default it is set to .01, I think, which causes the amplitude to be very large. If your events appear on the TR, then try setting it to the TR. 2) When I compare the results of this analysis to results obtained with FSL or SPM, I find that the spatial pattern of beta/t-stats is very similar, but the t-stats have a noticeably reduced magnitude across the brain. Is there anything that may differ about FS-FAST's implementation of the GLM, such that t-stats would differ? You might try turning off the whitening (--no-whiten I think). 3) I saw in a ppt presentation on FS-FAST that the option -hpf can be used to add a highpass temporal filter to the model. However, when I use this option with mkanalysis-new, the script says that the flag isn't recognized. Is there another way to add such a filter? It's in the 5.X version. doug Thanks in advance for any help. Cheers, Ben On Mon, Sep 5, 2011 at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 1 Date: Sun, 4 Sep 2011 13:15:51 -0400 From: Benjamin Matthew Deen bd...@mit.edu Subject: [Freesurfer] FS-FAST modeling question To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: d0755b22ea5ed64c941ed568237aec8d1764dcc...@expo11.exchange.mit.edu Content-Type: text/plain; charset=us-ascii Hi, I'm trying to run a model in fs-fast using no intensity normalization and no autocorrelation correction, for the purpose of comparing results with other software packages, and comparing results with/without autocorrelation correction. However, I haven't been able to get this to work so far. I've tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these don't seem to have any effect on the results: noinorm doesn't change the beta values, and nowhiten doesn't change either betas or t-stats, at all. The commands I'm using are: mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm -nowhiten mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1 -c 2 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2 -c 1 mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1 -a 2 -c 0
[Freesurfer] refeventdur in mkanalysis-sess
Hi, I am making an analysis in freesurfer 5.1 using mkanalysis-sess and I am a bit confused about the flag refeventdur. In the help it is said that it should be set to the event duration if the events have similar durations. I have four conditions that last for 16 second each in a block design paradigm, but my fixation condition lasts for 8 second. What should I set the refeventdur to? Also I have an event related design with variable fixation durations. what should it be in that condition? How about if I have an event related design with variable stimulus durations? How does this value influence the design matrix? Thanks, Maryam ___ 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] refeventdur in mkanalysis-sess
Hi Maryam, yes, I admit, that is a confusing option. The events that the help refers to only apply to task events (not the fixation). In your case, you would just set it to 16 sec. doug On 9/8/11 10:55 PM, Maryam Vaziri Pashkam wrote: Hi, I am making an analysis in freesurfer 5.1 using mkanalysis-sess and I am a bit confused about the flag refeventdur. In the help it is said that it should be set to the event duration if the events have similar durations. I have four conditions that last for 16 second each in a block design paradigm, but my fixation condition lasts for 8 second. What should I set the refeventdur to? Also I have an event related design with variable fixation durations. what should it be in that condition? How about if I have an event related design with variable stimulus durations? How does this value influence the design matrix? Thanks, Maryam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] structure volume
Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of structures for the same brain. Just trying to understand why that is? best, AJ ___ 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.
