Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis
External Email - Use Caution Thanks. On Tue, Oct 15, 2019 at 5:00 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Correct > > On 10/15/2019 9:38 AM, Keri Woods wrote: > > External Email - Use Caution > Hi Doug > > Thank you very much for the very helpful reply! It worked perfectly and > was exactly what I needed. I assume that these are the clusters after > cluster-level correction for multiple comparison since --csd is used? > > Thanks, > Keri > > On Tue, Oct 15, 2019 at 4:17 AM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> Sorry for the delay ... >> >> First, run selxavg3-sess with -fwhm ( you might need to delete the >> bold/analysis folder to get it to re-run). >> >> cd session/bold/analyis >> There will be a filed called fwhm.dat. Look in that. Depending upon how >> much you smoothed it might be something like 10.395. This is the FWHM in >> mm. Next, you can run something like the following command >> >> mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd >> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf >> --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot >> --thmin T --sign abs --subject fsaverage --cwpvalthresh .05 >> >> Note that the subject must be fsaverage because the tables were computed >> with fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395, >> but round up to 11). TT refers to the cluster forming threshold (eg, p<.001 >> would be 30), and so --thmin T would be 3. "abs" in the path to the CSD >> file indicates that you want to use an unsigned (absolute) value; you can >> also use pos and neg. --cwpvalthresh .05 means to filter out any clusters >> that are not significant at p=0.05. The cluster table will be in >> contrast.sum.dat >> >> doug >> >> >> On 10/3/2019 7:52 AM, Keri Woods wrote: >> >> External Email - Use Caution >> Hi >> >> From the 1st level analysis of an fMRI study I'm trying to extract the >> size of the clusters of activation from each subject, but don't know how to >> go about this. I know that for the group analysis you can get the cluster >> sizes from the output from mri_glm-sim. Is there a way to run the multiple >> comparison correction on the first level analysis in order to get this >> table? Or is there another way of getting the cluster sizes? >> >> Any help would be much appreciated. >> >> Thank you, >> Keri >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis
External Email - Use Caution Hi Doug Thank you very much for the very helpful reply! It worked perfectly and was exactly what I needed. I assume that these are the clusters after cluster-level correction for multiple comparison since --csd is used? Thanks, Keri On Tue, Oct 15, 2019 at 4:17 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Sorry for the delay ... > > First, run selxavg3-sess with -fwhm ( you might need to delete the > bold/analysis folder to get it to re-run). > > cd session/bold/analyis > There will be a filed called fwhm.dat. Look in that. Depending upon how > much you smoothed it might be something like 10.395. This is the FWHM in > mm. Next, you can run something like the following command > > mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd > $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf > --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot > --thmin T --sign abs --subject fsaverage --cwpvalthresh .05 > > Note that the subject must be fsaverage because the tables were computed > with fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395, > but round up to 11). TT refers to the cluster forming threshold (eg, p<.001 > would be 30), and so --thmin T would be 3. "abs" in the path to the CSD > file indicates that you want to use an unsigned (absolute) value; you can > also use pos and neg. --cwpvalthresh .05 means to filter out any clusters > that are not significant at p=0.05. The cluster table will be in > contrast.sum.dat > > doug > > > On 10/3/2019 7:52 AM, Keri Woods wrote: > > External Email - Use Caution > Hi > > From the 1st level analysis of an fMRI study I'm trying to extract the > size of the clusters of activation from each subject, but don't know how to > go about this. I know that for the group analysis you can get the cluster > sizes from the output from mri_glm-sim. Is there a way to run the multiple > comparison correction on the first level analysis in order to get this > table? Or is there another way of getting the cluster sizes? > > Any help would be much appreciated. > > Thank you, > Keri > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS-FAST: cluster size from 1st level analysis
External Email - Use Caution Hi From the 1st level analysis of an fMRI study I'm trying to extract the size of the clusters of activation from each subject, but don't know how to go about this. I know that for the group analysis you can get the cluster sizes from the output from mri_glm-sim. Is there a way to run the multiple comparison correction on the first level analysis in order to get this table? Or is there another way of getting the cluster sizes? Any help would be much appreciated. Thank you, Keri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSFAST group analysis problem: dimension mismatch between y and X
External Email - Use Caution Hi Freesurfer experts I'm having a problem running an FSFAST group analysis. When I try to run the second level GLM, I get the following error: keri@buddha:~/audio_108_no_stc_tau1,5$ mri_glmfit --y ~/audio/all/audio.lh/tones/ces.nii.gz --wls ~/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd --C groupdiff.mtx --surface fsaverage lh --glmdir all_tones_left_glm.wls --nii.gz gdfRead(): reading 2groups.fsgd INFO: gd2mtx_method is dods Reading source surface /home/keri/recon_all/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/keri/audio_108_no_stc_tau1,5 cmdline mri_glmfit.bin --y /home/keri/audio/all/audio.lh/tones/ces.nii.gz --wls /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd --C groupdiff.mtx --surface fsaverage lh --glmdir all_tones_left_glm.wls --nii.gz sysname Linux hostname buddha machine x86_64 user keri FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/home/keri/audio/all/audio.lh/tones/ces.nii.gz logyflag 0 usedti 0 FSGD 2groups.fsgd labelmask /home/keri/recon_all/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir all_tones_left_glm.wls IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory all_tones_left_glm.wls Loading y from /home/keri/audio/all/audio.lh/tones/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to all_tones_left_glm.wls/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.34783 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 66097 voxels in mask Saving mask to all_tones_left_glm.wls/mask.nii.gz Reshaping mriglm->mask... search space = 31233.070725 ERROR: dimension mismatch between y and X. y has 116 inputs, X has 108 rows. 108 is the number of subjects that I have. I can see that the y file with 116 inputs is /home/keri/audio/all/audio.lh/tones/ces.nii.gz , and checking the dimension of it, it confirms that it is a 4D matrix with the 4th dimension of 116. It seems as if this file is created during isxoconcat-sess, and I have checked and the session ID file being used here has only 108 entries. It appears that 108 subjects are being used in this step, as part of the output is: ninputs = 108 Checking inputs nframestot = 108 Allocing output Done allocing nframes = 108 I think that a source of the error could be the fact that at one time I did have 116 subjects. I've created a new folder, copying in the unpacked files for each subject, and repeating from the preprocessing step, but this doesn't make any difference. Is there are chance that there's a file outside the functional directory that has stored this 116? Any help is greatly appreciated. Best wishes, Keri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSFAST poor registration
External Email - Use Caution Good thing it's not the software :) Also makes it easier for me to fix. In my script there was one tiny mistake - the anatomical image for one subject was repeated each time instead of using the files for different subjects. I ran recon-all 100+ times on the same subject!! Checking the registration was definitely worthwhile. Thanks again for the help, it made me look at the problem in a different. On Fri, Jan 25, 2019 at 6:34 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Yes, that file is the only thing linking the functional to the anatomical. > It's too bad you messed up the files, but I'm relieved it was not my > software:). > > On 1/25/19 5:09 AM, Keri Woods wrote: > > External Email - Use Caution > Hi Douglas > > Thanks very much for getting back to me. I created new separate > directories and re-processed one of the problem subjects individually, and > the registration worked well. So the problem is that the anatomical and > functional images come from different subjects. But I've checked and the > subjectname files are correct. That's the only thing linking the anatomical > and functional images? Thanks very much, you've helped me a lot. Now I just > have to go and see where I mixed up the files! > > Thanks again, > Keri > > On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> Can you tar up the anatomical and functional analyses and send them to >> me through our filedrop? >> >> https://gate.nmr.mgh.harvard.edu/filedrop2/ >> >> when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu >> >> >> On 1/23/19 5:57 AM, Keri Woods wrote: >> > >> > External Email - Use Caution >> > >> > I meant some are nearly perfect. >> > >> > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods > > <mailto:keri.wo...@gmail.com>> wrote: >> > >> > Hi Douglas >> > >> > Thanks for the response. >> > >> > No, some of the registrations are fine. Some are close, but not >> > perfect, while others are very bad. >> > >> > I've checked the subjectname file for some subjects with poor >> > registration (eg 20_101), and they are correct. >> > >> > Thanks, >> > Keri >> > >> > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. >> > mailto:dgr...@mgh.harvard.edu>> wrote: >> > >> > Are you saying that all of them have bad registrations? Some >> > of them >> > (eg, 20_1, 20_10) look like they should be good. Others (eg, >> > 20_101) >> > look like they could be bad. For the bad ones, are you totally >> > sure that >> > the subjetname file has the correct name of the subject? >> > >> > On 1/21/19 3:19 AM, Keri Woods wrote: >> > > >> > > External Email - Use Caution >> > > >> > > Hi Douglas >> > > >> > > Thank you for your reply. >> > > >> > > I'm using >> > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a >> > > >> > > I am using whole brain data. The functional and structural >> > images were >> > > acquired in different sessions on the same day, I don't know >> > if that >> > > complicated things? Each subject has 2 runs of the same task. >> > > >> > > This is what I get after running the command in the format of >> > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold >> > -per-run -bbr-sum >> > > >> > > 20_1 013 0.5155 >> > > 20_1 014 0.5090 >> > > 20_10 013 0.5247 >> > > 20_10 014 0.5229 >> > > 20_100 038 0.8420 >> > > 20_100 040 0.8443 >> > > 20_101 008 0.9052 >> > > 20_101 010 0.9289 >> > > 20_102 058 0.6924 >> > > 20_102 059 0.6902 >> > > 20_103 045 0.9778 >> > > 20_103 046 0.9931 >> > > 20_104 010 0.9324 >> > > 20_104 012 0.9413 >> > > 20_105 0
Re: [Freesurfer] FSFAST poor registration
External Email - Use Caution Hi Douglas Thanks very much for getting back to me. I created new separate directories and re-processed one of the problem subjects individually, and the registration worked well. So the problem is that the anatomical and functional images come from different subjects. But I've checked and the subjectname files are correct. That's the only thing linking the anatomical and functional images? Thanks very much, you've helped me a lot. Now I just have to go and see where I mixed up the files! Thanks again, Keri On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Can you tar up the anatomical and functional analyses and send them to > me through our filedrop? > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu > > > On 1/23/19 5:57 AM, Keri Woods wrote: > > > > External Email - Use Caution > > > > I meant some are nearly perfect. > > > > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods > <mailto:keri.wo...@gmail.com>> wrote: > > > > Hi Douglas > > > > Thanks for the response. > > > > No, some of the registrations are fine. Some are close, but not > > perfect, while others are very bad. > > > > I've checked the subjectname file for some subjects with poor > > registration (eg 20_101), and they are correct. > > > > Thanks, > > Keri > > > > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> wrote: > > > > Are you saying that all of them have bad registrations? Some > > of them > > (eg, 20_1, 20_10) look like they should be good. Others (eg, > > 20_101) > > look like they could be bad. For the bad ones, are you totally > > sure that > > the subjetname file has the correct name of the subject? > > > > On 1/21/19 3:19 AM, Keri Woods wrote: > > > > > > External Email - Use Caution > > > > > > Hi Douglas > > > > > > Thank you for your reply. > > > > > > I'm using > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > > > > > I am using whole brain data. The functional and structural > > images were > > > acquired in different sessions on the same day, I don't know > > if that > > > complicated things? Each subject has 2 runs of the same task. > > > > > > This is what I get after running the command in the format of > > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold > > -per-run -bbr-sum > > > > > > 20_1 013 0.5155 > > > 20_1 014 0.5090 > > > 20_10 013 0.5247 > > > 20_10 014 0.5229 > > > 20_100 038 0.8420 > > > 20_100 040 0.8443 > > > 20_101 008 0.9052 > > > 20_101 010 0.9289 > > > 20_102 058 0.6924 > > > 20_102 059 0.6902 > > > 20_103 045 0.9778 > > > 20_103 046 0.9931 > > > 20_104 010 0.9324 > > > 20_104 012 0.9413 > > > 20_105 013 0.8754 > > > 20_105 014 0.8937 > > > 20_106 047 0.4433 > > > 20_106 048 0.4377 > > > 20_107 008 0.9178 > > > 20_107 010 0.9238 > > > 20_11 013 0.7631 > > > 20_11 014 0.7615 > > > 20_110 048 0.7687 > > > 20_110 049 0.7549 > > > 20_112 013 0.8821 > > > 20_112 014 0.9161 > > > 20_113 052 0.7689 > > > 20_113 053 0.7757 > > > 20_116 046 1.0072 > > > 20_116 047 1.0256 > > > 20_117 008 0.7742 > > > 20_117 010 0.7826 > > > 20_119 013 0.7929 > > > 20_119 014 0.7854 > > > 20_120 048 0.5090 > > > 20_120 049 0.4973 > > > 20_126 047 0.8285 > > > 20_126 048 0.8281 > > > 20_128 046 0.9580 > > > 20_128 047 0.9314 > > > 20_
Re: [Freesurfer] FSFAST poor registration
External Email - Use Caution I meant some are nearly perfect. On Wed, Jan 23, 2019 at 11:49 AM Keri Woods wrote: > Hi Douglas > > Thanks for the response. > > No, some of the registrations are fine. Some are close, but not perfect, > while others are very bad. > > I've checked the subjectname file for some subjects with poor registration > (eg 20_101), and they are correct. > > Thanks, > Keri > > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> Are you saying that all of them have bad registrations? Some of them >> (eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101) >> look like they could be bad. For the bad ones, are you totally sure that >> the subjetname file has the correct name of the subject? >> >> On 1/21/19 3:19 AM, Keri Woods wrote: >> > >> > External Email - Use Caution >> > >> > Hi Douglas >> > >> > Thank you for your reply. >> > >> > I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a >> > >> > I am using whole brain data. The functional and structural images were >> > acquired in different sessions on the same day, I don't know if that >> > complicated things? Each subject has 2 runs of the same task. >> > >> > This is what I get after running the command in the format of >> > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run >> -bbr-sum >> > >> > 20_1 013 0.5155 >> > 20_1 014 0.5090 >> > 20_10 013 0.5247 >> > 20_10 014 0.5229 >> > 20_100 038 0.8420 >> > 20_100 040 0.8443 >> > 20_101 008 0.9052 >> > 20_101 010 0.9289 >> > 20_102 058 0.6924 >> > 20_102 059 0.6902 >> > 20_103 045 0.9778 >> > 20_103 046 0.9931 >> > 20_104 010 0.9324 >> > 20_104 012 0.9413 >> > 20_105 013 0.8754 >> > 20_105 014 0.8937 >> > 20_106 047 0.4433 >> > 20_106 048 0.4377 >> > 20_107 008 0.9178 >> > 20_107 010 0.9238 >> > 20_11 013 0.7631 >> > 20_11 014 0.7615 >> > 20_110 048 0.7687 >> > 20_110 049 0.7549 >> > 20_112 013 0.8821 >> > 20_112 014 0.9161 >> > 20_113 052 0.7689 >> > 20_113 053 0.7757 >> > 20_116 046 1.0072 >> > 20_116 047 1.0256 >> > 20_117 008 0.7742 >> > 20_117 010 0.7826 >> > 20_119 013 0.7929 >> > 20_119 014 0.7854 >> > 20_120 048 0.5090 >> > 20_120 049 0.4973 >> > 20_126 047 0.8285 >> > 20_126 048 0.8281 >> > 20_128 046 0.9580 >> > 20_128 047 0.9314 >> > 20_130 047 0.9439 >> > 20_130 048 0.9425 >> > 20_132 047 0.8550 >> > 20_132 048 0.8558 >> > 20_134_1 013 0.5716 >> > 20_134_1 015 0.5744 >> > 20_135 011 0.8357 >> > 20_135 012 0.8401 >> > 20_136 044 0.9995 >> > 20_136 045 0.9604 >> > 20_137 047 0.7922 >> > 20_137 048 0.7990 >> > 20_142 047 0.5282 >> > 20_142 048 0.5278 >> > 20_144 013 0.8755 >> > 20_144 014 0.8838 >> > 20_146 047 0.7997 >> > 20_146 048 0.7895 >> > 20_149 049 0.9251 >> > 20_149 050 0.9408 >> > 20_151 048 0.5905 >> > 20_151 049 0.5519 >> > 20_152 048 0.9024 >> > 20_152 049 0.9021 >> > 20_155 048 0.5285 >> > 20_155 049 0.5324 >> > 20_156 048 0.8883 >> > 20_156 049 0.9267 >> > 20_158 048 0.5404 >> > 20_158 049 0.5297 >> > 20_159 048 0.8021 >> > 20_160 013 0.5002 >> > 20_160 014 0.4942 >> > 20_162 047 0.5401 >> > 20_162 048 0.5401 >> > 20_164 047 0.8944 >> > 20_164 048 0.8940 >> > 20_165 047 0.9163 >> > 20_165 048 0.9077 >> > 20_166 045 0.8787 >> > 20_166 046 0.8848 >> > 20_167 050 0.8428 >> > 20_167 051 0.8442 >> > 20_169 049 0.9407 >> > 20_169 050 0.9462 >> > 20_170 047 0.8921 >> > 20_170 048 0.9113 >> > 20_171 013 0.9060 >> > 20_171 014 0.9060 >> > 20_173 048 0.9193 >> > 20_173 049 0.9141 >> > 20_177 048 0.8695 >> > 20_177
Re: [Freesurfer] FSFAST poor registration
External Email - Use Caution Hi Douglas Thanks for the response. No, some of the registrations are fine. Some are close, but not perfect, while others are very bad. I've checked the subjectname file for some subjects with poor registration (eg 20_101), and they are correct. Thanks, Keri On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Are you saying that all of them have bad registrations? Some of them > (eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101) > look like they could be bad. For the bad ones, are you totally sure that > the subjetname file has the correct name of the subject? > > On 1/21/19 3:19 AM, Keri Woods wrote: > > > > External Email - Use Caution > > > > Hi Douglas > > > > Thank you for your reply. > > > > I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > > > I am using whole brain data. The functional and structural images were > > acquired in different sessions on the same day, I don't know if that > > complicated things? Each subject has 2 runs of the same task. > > > > This is what I get after running the command in the format of > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum > > > > 20_1 013 0.5155 > > 20_1 014 0.5090 > > 20_10 013 0.5247 > > 20_10 014 0.5229 > > 20_100 038 0.8420 > > 20_100 040 0.8443 > > 20_101 008 0.9052 > > 20_101 010 0.9289 > > 20_102 058 0.6924 > > 20_102 059 0.6902 > > 20_103 045 0.9778 > > 20_103 046 0.9931 > > 20_104 010 0.9324 > > 20_104 012 0.9413 > > 20_105 013 0.8754 > > 20_105 014 0.8937 > > 20_106 047 0.4433 > > 20_106 048 0.4377 > > 20_107 008 0.9178 > > 20_107 010 0.9238 > > 20_11 013 0.7631 > > 20_11 014 0.7615 > > 20_110 048 0.7687 > > 20_110 049 0.7549 > > 20_112 013 0.8821 > > 20_112 014 0.9161 > > 20_113 052 0.7689 > > 20_113 053 0.7757 > > 20_116 046 1.0072 > > 20_116 047 1.0256 > > 20_117 008 0.7742 > > 20_117 010 0.7826 > > 20_119 013 0.7929 > > 20_119 014 0.7854 > > 20_120 048 0.5090 > > 20_120 049 0.4973 > > 20_126 047 0.8285 > > 20_126 048 0.8281 > > 20_128 046 0.9580 > > 20_128 047 0.9314 > > 20_130 047 0.9439 > > 20_130 048 0.9425 > > 20_132 047 0.8550 > > 20_132 048 0.8558 > > 20_134_1 013 0.5716 > > 20_134_1 015 0.5744 > > 20_135 011 0.8357 > > 20_135 012 0.8401 > > 20_136 044 0.9995 > > 20_136 045 0.9604 > > 20_137 047 0.7922 > > 20_137 048 0.7990 > > 20_142 047 0.5282 > > 20_142 048 0.5278 > > 20_144 013 0.8755 > > 20_144 014 0.8838 > > 20_146 047 0.7997 > > 20_146 048 0.7895 > > 20_149 049 0.9251 > > 20_149 050 0.9408 > > 20_151 048 0.5905 > > 20_151 049 0.5519 > > 20_152 048 0.9024 > > 20_152 049 0.9021 > > 20_155 048 0.5285 > > 20_155 049 0.5324 > > 20_156 048 0.8883 > > 20_156 049 0.9267 > > 20_158 048 0.5404 > > 20_158 049 0.5297 > > 20_159 048 0.8021 > > 20_160 013 0.5002 > > 20_160 014 0.4942 > > 20_162 047 0.5401 > > 20_162 048 0.5401 > > 20_164 047 0.8944 > > 20_164 048 0.8940 > > 20_165 047 0.9163 > > 20_165 048 0.9077 > > 20_166 045 0.8787 > > 20_166 046 0.8848 > > 20_167 050 0.8428 > > 20_167 051 0.8442 > > 20_169 049 0.9407 > > 20_169 050 0.9462 > > 20_170 047 0.8921 > > 20_170 048 0.9113 > > 20_171 013 0.9060 > > 20_171 014 0.9060 > > 20_173 048 0.9193 > > 20_173 049 0.9141 > > 20_177 048 0.8695 > > 20_177 049 0.8600 > > 20_178 048 1.0327 > > 20_178 049 0.8979 > > 20_180 045 0.7999 > > 20_180 046 0.8002 > > 20_182 047 0.9135 > > 20_182 048 0.9130 > > 20_184 048 0.9842 > > 20_184 049 0.9960 > > 20_185 046 0.9640 > > 20_185 047 0.9514 > > 20_187 048 0.8134 > > 20_187 049 0.8082 > > 20_189 047 1.0063 > > 20_189 048 0.9701 > > 20_19 013 0.8485 > > 20_19 014 0.8534 > > 20_190 047 0.9279 > > 20_190 048 0.9169 > > 20_191 046 0.9586 > > 20_191
Re: [Freesurfer] FSFAST poor registration
93 052 0.7792 20_293 053 0.7772 20_3 017 0.8530 20_3 018 0.8501 20_40 013 0.9392 20_40 014 0.9787 20_41 013 0.9562 20_41 014 0.9547 20_44 013 0.8725 20_44 014 0.8872 20_51 013 0.9420 20_51 014 0.9417 20_55 013 0.9796 20_55 014 0.9837 20_58 013 0.9677 20_58 014 0.9506 20_59 013 0.9180 20_59 014 0.9157 20_69 013 0.9265 20_69 014 0.9283 20_74 014 0.9476 20_74 015 0.9201 20_78 012 0.9822 20_78 013 0.9501 20_81 013 0.8664 20_81 014 0.8693 20_84 013 0.8827 20_84 014 0.9196 20_86 016 0.9138 20_86 017 0.9152 20_88 039 0.9905 20_88 041 1.0168 20_90 049 0.8263 20_90 050 1.0208 20_95 008 0.8892 20_95 010 0.9359 20_96 013 0.9191 20_96 014 0.9326 20_97 008 0.9569 20_97 010 0.9731 20_98 008 0.9317 20_98 012 0.9409 20_PHRU047 0.7797 20_PHRU048 0.7894 So the registration is really poor. I've visually checked the registration for many of the subjects, and the functional data isn't left-right reversed, I've also checked some of the subjectname files (which I created by running a script) and they are correct. I'm new to Freesurfer, so maybe I've made a mistake somewhere? I'm been following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial Thanks, Keri On Fri, Jan 18, 2019 at 6:44 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > What version of FS are you using? version 6 initializes with mri_coreg > (the FS equivalent of spm_coreg). On whole-brain data, I've found this to > be very robust. Is your data whole-brain? > > On 1/18/19 5:10 AM, Keri Woods wrote: > > External Email - Use Caution > Hi > > I have a problem very similar to this one: > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html > > I've tried the suggestions given there, but it didn't fix my problem. > > I'm running the FSFAST preproc-sess stream and the quality of the > registration is very poor for most of the subjects. > > I've tried initializing the registration differently, using bbregister > with --init-fsl, --init-spm and init-header, which didn't improve the > results at all. > > I've also tried register-sess with --init-fsl, --init-spm and init-header, > as well as spmregister-sess and fslregister-sess. > > Is there anything else I could try? > > Using the SPM GUI, the registration was fine, so I thought that > spmregister-sess would have been an improvement, but it wasn't. Is there > anyway I can import the registration obtained using the SPM GUI? > > Thanks for your help. > > Thanks, > Keri > > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSFAST poor registration
External Email - Use Caution Hi I have a problem very similar to this one: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html I've tried the suggestions given there, but it didn't fix my problem. I'm running the FSFAST preproc-sess stream and the quality of the registration is very poor for most of the subjects. I've tried initializing the registration differently, using bbregister with --init-fsl, --init-spm and init-header, which didn't improve the results at all. I've also tried register-sess with --init-fsl, --init-spm and init-header, as well as spmregister-sess and fslregister-sess. Is there anything else I could try? Using the SPM GUI, the registration was fine, so I thought that spmregister-sess would have been an improvement, but it wasn't. Is there anyway I can import the registration obtained using the SPM GUI? Thanks for your help. Thanks, Keri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with checking registration quality using tkregister-sess: if: Expression Syntax.
External Email - Use Caution Hi Everyone I've managed to fix my problem. In case anyone else has the same problem, the problem was that the subject name was repeated twice in the subjectname file within the subject_ID (in my case 20_1) folder. Best wishes, Keri On Thu, Jan 10, 2019 at 11:57 AM Keri Woods wrote: > Hi > > > I’m having a problem that I’m hoping someone could help me with. > > > I’m trying to check the quality of the alignment of structural and > functional data, using the command: > > > tkregister-sess -s 20_1 -fsd bold -per-run > > > where 20_1 is the subject ID. Nothing opens, and I get the following error: > > > > > -- > > tkregister-sess logfile is /home/keri/audio2/log/tkregister-sess.log > > -- > > Session: 20_1 > > if: Expression Syntax. > > > > > > I’ve opened the log file, which doesn’t shed much light on the problem. > Its contents are: > > > > > > tkregister-sess log file > > $Id: tkregister-sess,v 1.42 2015/12/10 22:51:31 zkaufman Exp $ > > > setenv SUBJECTS_DIR /home/keri/recon_all/subjects > > cd /home/keri/audio > > /usr/local/freesurfer/fsfast/bin/tkregister-sess -s 20_1 -fsd bold -per-run > > > buddha > > /usr/local/freesurfer/bin/tkregister2 > > Session: 20_1 > > > > > The SUBJECTS_DIR show here is correct. > > > I’ve been looking through the archives, and someone suggested checking > whether tkmedit works when having problems with tkregister. I’ve done this, > and it works fine. > > > > > On a side note, when checking the quality of registration using the > command in the format of: > > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum > > > I get very poor results for many of the subjects (some of them are even > > 1, which I didn’t think was possible). Could this be part of the problem? > The subject 20_1 I used as a example did have a fairly good result (eg > 0.5090 for one run). > > > Thanks in advance. > > > Best wishes, > > Keri > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with checking registration quality using tkregister-sess: if: Expression Syntax.
External Email - Use Caution Hi I’m having a problem that I’m hoping someone could help me with. I’m trying to check the quality of the alignment of structural and functional data, using the command: tkregister-sess -s 20_1 -fsd bold -per-run where 20_1 is the subject ID. Nothing opens, and I get the following error: -- tkregister-sess logfile is /home/keri/audio2/log/tkregister-sess.log -- Session: 20_1 if: Expression Syntax. I’ve opened the log file, which doesn’t shed much light on the problem. Its contents are: tkregister-sess log file $Id: tkregister-sess,v 1.42 2015/12/10 22:51:31 zkaufman Exp $ setenv SUBJECTS_DIR /home/keri/recon_all/subjects cd /home/keri/audio /usr/local/freesurfer/fsfast/bin/tkregister-sess -s 20_1 -fsd bold -per-run buddha /usr/local/freesurfer/bin/tkregister2 Session: 20_1 The SUBJECTS_DIR show here is correct. I’ve been looking through the archives, and someone suggested checking whether tkmedit works when having problems with tkregister. I’ve done this, and it works fine. On a side note, when checking the quality of registration using the command in the format of: tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum I get very poor results for many of the subjects (some of them are even > 1, which I didn’t think was possible). Could this be part of the problem? The subject 20_1 I used as a example did have a fairly good result (eg 0.5090 for one run). Thanks in advance. Best wishes, Keri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
