Re: [Freesurfer] Reasons for problems with resampling issues
Dear Douglas thanks a lot for your advice. I tried it, but only one volume of the stack was read. I tried to use the --frame option, but it does not work. How can I force mri_segstats with the --frame option so that all 53 volumes of the stack are read? Thanks in advance Regards Jürgen Am 02.07.15 14:44 schrieb Douglas N Greve unter freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu: There are inevitable issues around the boundaries of the cluster. For small clusters, this can be a big deal. I would probably just use the fsaverage clusters on the control group after they have been mapped to fsaverage space (ie, run mris_preproc on the control group to get a stack, smooth it, then run mri_segstats with the stack as the input and the ocn.mgh file as the --seg. doug On 07/02/2015 03:21 AM, Jürgen Hänggi wrote: Dear FS experts in a former email http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg23322.htm l it has been recommended that we should not map clusters found in an analysis in the standard space back to the individual space due to resampling issues. In one of our study, we computed a correlation across patients and controlls and get MC simulation corrected clusters, the individual values of it can be found in the .y.ocn.dat file. A reviewer suggested to do the correlation only across the patient group and then transform these clusters into the native space in order to extract the values within these clusters for the control group. Therefore we would like to know the exact reason why this resampling is not recommended. Is it related to the fact that the transform from the native to the standard space is not one-to-one? What you recommend to answer to this reviewer point? Thanks in advance Best regards Jürgen Hänggi - -- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. - -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Reasons for problems with resampling issues
Dear FS experts in a former email http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg23322.html it has been recommended that we should not map clusters found in an analysis in the standard space back to the individual space due to resampling issues. In one of our study, we computed a correlation across patients and controlls and get MC simulation corrected clusters, the individual values of it can be found in the .y.ocn.dat file. A reviewer suggested to do the correlation only across the patient group and then transform these clusters into the native space in order to extract the values within these clusters for the control group. Therefore we would like to know the exact reason why this resampling is not recommended. Is it related to the fact that the transform from the native to the standard space is not one-to-one? What you recommend to answer to this reviewer point? Thanks in advance Best regards Jürgen Hänggi --- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. --- ___ 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] Reasons for problems with resampling issues
There are inevitable issues around the boundaries of the cluster. For small clusters, this can be a big deal. I would probably just use the fsaverage clusters on the control group after they have been mapped to fsaverage space (ie, run mris_preproc on the control group to get a stack, smooth it, then run mri_segstats with the stack as the input and the ocn.mgh file as the --seg. doug On 07/02/2015 03:21 AM, Jürgen Hänggi wrote: Dear FS experts in a former email http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg23322.html it has been recommended that we should not map clusters found in an analysis in the standard space back to the individual space due to resampling issues. In one of our study, we computed a correlation across patients and controlls and get MC simulation corrected clusters, the individual values of it can be found in the ….y.ocn.dat file. A reviewer suggested to do the correlation only across the patient group and then transform these clusters into the native space in order to extract the values within these clusters for the control group. Therefore we would like to know the exact reason why this resampling is not recommended. Is it related to the fact that the transform from the native to the standard space is not one-to-one? What you recommend to answer to this reviewer point? Thanks in advance Best regards Jürgen Hänggi --- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
