[Freesurfer] rcbf-prep outputting negative values
Hello, I have pcASL data from a Siemens 3T scanner which I would like to process using the provided rcbf-prep command. The process completes smoothly without error. However when I inspect my roi.dat file, I observe that all the ROI values are actually negative, and seem to be beyond physiological CBF range (~60-120 ml/100g/min). The roi.dat file is pasted below. Would there be any reason to suspect that the tag-control subtraction might be running inverted? I was trying to find a way to customize the command, but seems like there’s no option to specifying the order of tag and control. Any help would be appreciated! Best, Asif # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ # cmdline mri_segstats --seg /www/data/fMRI/subjects/PV/mri/aparc+aseg.mgz --ctab /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.table --i /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/rcbf.anat.nii --sum /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.dat # sysname Darwin # hostname MBP-4.local # machine x86_64 # user asif # anatomy_type volume # # SegVolFile /www/data/fMRI/subjects/PV/mri/aparc+aseg.mgz # SegVolFileTimeStamp 2014/10/21 08:43:42 # ColorTable /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.table # ColorTableTimeStamp 2014/10/22 15:52:27 # InVolFile /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/rcbf.anat.nii # InVolFileTimeStamp 2014/10/22 16:00:34 # InVolFrame 0 # Only reporting non-empty segmentations # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader Mean # TableCol 6 FieldName Intensity Mean # TableCol 6 Units unknown # TableCol 7 ColHeader StdDev # TableCol 7 FieldName Itensity StdDev # TableCol 7 Units unknown # TableCol 8 ColHeader Min # TableCol 8 FieldName Intensity Min # TableCol 8 Units unknown # TableCol 9 ColHeader Max # TableCol 9 FieldName Intensity Max # TableCol 9 Units unknown # TableCol 10 ColHeader Range # TableCol 10 FieldName Intensity Range # TableCol 10 Units unknown # NRows 114 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 0 15692031 15692031.0 Unknown -74.0533 149.7173 -409.6000 212.1609 621.7609 2 2223002 223002.0 Left-Cerebral-White-Matter -225.7412 41.4942 -378.468443.0771 421.5454 3 4 5142 5142.0 Left-Lateral-Ventricle -213.5301 25.6550 -268.4635 -140.5092 127.9543 4 5 210 210.0 Left-Inf-Lat-Vent -250.1857 11.2349 -268.3093 -227.502840.8065 5 7 1220112201.0 Left-Cerebellum-White-Matter-184.3329 132.5210 -314.1348 0. 314.1348 6 8 3882238822.0 Left-Cerebellum-Cortex -106.5107 126.4406 -397.5404 0. 397.5404 7 10 7802 7802.0 Left-Thalamus-Proper-256.3931 10.4379 -280.3882 -205.426774.9615 8 11 4000 4000.0 Left-Caudate-202.6371 20.4855 -256.5304 -151.9264 104.6040 9 12 6375 6375.0 Left-Putamen-225.6037 14.5390 -274.2597 -175.457798.8020 10 13 1502 1502.0 Left-Pallidum -253.1898 12.3024 -277.3420 -185.777591.5645 11 14 550 550.0 3rd-Ventricle -225.0951 31.5825 -306.7295 -134.6138 172.1157 12 15 964 964.0 4th-Ventricle -212.5151 112.4167 -288.3225 0. 288.3225 13 16 1818618186.0 Brain-Stem -234.2281 112.8928 -319.7348 0. 319.7348 14 17 4114 4114.0 Left-Hippocampus-261.7396 17.4063 -339.8024 -223.4028 116.3996 15 18 1513 1513.0 Left-Amygdala -253.4237 8.8525 -288.2225 -232.877755.3447 16 24 847 847.0 CSF -257.5531 13.5256 -300.9257 -212.227988.6977 17 26 535 535.0 Left-Accumbens-area -227.1246 45.3633 -360.7124 -138.9498 221.7626 18 28 3786 3786.0 Left-VentralDC -270.4991 24.1379 -308.4358 -148.3388 160.0970 19 3035 35.0 Left-vessel -239.3001 10.2992 -259.7188 -227.277732.4411 20 31 1442 1442.0 Left-choroid-plexus
Re: [Freesurfer] rcbf-prep outputting negative values
I'm not sure that anyone is maintaining this code any more. However, you can try running mri_convert --nskip 1 asl.nii asl.skip.nii and then use asl.skip.nii as input. This just removes the 1st frame so that the tag/control will be in the expected order doug On 10/22/2014 10:29 AM, Asif Jamil wrote: > Hello, > > I have pcASL data from a Siemens 3T scanner which I would like to > process using the provided rcbf-prep command. The process completes > smoothly without error. However when I inspect my roi.dat file, I > observe that all the ROI values are actually negative, and seem to be > beyond physiological CBF range (~60-120 ml/100g/min). > > The roi.dat file is pasted below. Would there be any reason to suspect > that the tag-control subtraction might be running inverted? I was > trying to find a way to customize the command, but seems like there’s > no option to specifying the order of tag and control. > > Any help would be appreciated! > > Best, > Asif > > > > > # Title Segmentation Statistics > # > # generating_program mri_segstats > # cvs_version $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ > # cmdline mri_segstats --seg > /www/data/fMRI/subjects/PV/mri/aparc+aseg.mgz --ctab > /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.table --i > /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/rcbf.anat.nii --sum > /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.dat > # sysname Darwin > # hostname MBP-4.local > # machine x86_64 > # user asif > # anatomy_type volume > # > # SegVolFile /www/data/fMRI/subjects/PV/mri/aparc+aseg.mgz > # SegVolFileTimeStamp 2014/10/21 08:43:42 > # ColorTable /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.table > # ColorTableTimeStamp 2014/10/22 15:52:27 > # InVolFile > /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/rcbf.anat.nii > # InVolFileTimeStamp 2014/10/22 16:00:34 > # InVolFrame 0 > # Only reporting non-empty segmentations > # VoxelVolume_mm3 1 > # TableCol 1 ColHeader Index > # TableCol 1 FieldName Index > # TableCol 1 Units NA > # TableCol 2 ColHeader SegId > # TableCol 2 FieldName Segmentation Id > # TableCol 2 Units NA > # TableCol 3 ColHeader NVoxels > # TableCol 3 FieldName Number of Voxels > # TableCol 3 Units unitless > # TableCol 4 ColHeader Volume_mm3 > # TableCol 4 FieldName Volume > # TableCol 4 Units mm^3 > # TableCol 5 ColHeader StructName > # TableCol 5 FieldName Structure Name > # TableCol 5 Units NA > # TableCol 6 ColHeader Mean > # TableCol 6 FieldName Intensity Mean > # TableCol 6 Units unknown > # TableCol 7 ColHeader StdDev > # TableCol 7 FieldName Itensity StdDev > # TableCol 7 Units unknown > # TableCol 8 ColHeader Min > # TableCol 8 FieldName Intensity Min > # TableCol 8 Units unknown > # TableCol 9 ColHeader Max > # TableCol 9 FieldName Intensity Max > # TableCol 9 Units unknown > # TableCol 10 ColHeader Range > # TableCol 10 FieldName Intensity Range > # TableCol 10 Units unknown > # NRows 114 > # NTableCols 10 > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min > Max Range > 1 0 15692031 15692031.0 Unknown -74.0533 149.7173 -409.6000 212.1609 > 621.7609 > 2 2 223002 223002.0 Left-Cerebral-White-Matter -225.7412 41.4942 > -378.4684 43.0771 421.5454 > 3 4 5142 5142.0 Left-Lateral-Ventricle -213.5301 25.6550 -268.4635 > -140.5092 127.9543 > 4 5 210 210.0 Left-Inf-Lat-Vent -250.1857 11.2349 -268.3093 -227.5028 > 40.8065 > 5 7 12201 12201.0 Left-Cerebellum-White-Matter -184.3329 132.5210 > -314.1348 0. 314.1348 > 6 8 38822 38822.0 Left-Cerebellum-Cortex -106.5107 126.4406 -397.5404 > 0. 397.5404 > 7 10 7802 7802.0 Left-Thalamus-Proper -256.3931 10.4379 -280.3882 > -205.4267 74.9615 > 8 11 4000 4000.0 Left-Caudate -202.6371 20.4855 -256.5304 -151.9264 > 104.6040 > 9 12 6375 6375.0 Left-Putamen -225.6037 14.5390 -274.2597 -175.4577 > 98.8020 > 10 13 1502 1502.0 Left-Pallidum -253.1898 12.3024 -277.3420 -185.7775 > 91.5645 > 11 14 550 550.0 3rd-Ventricle -225.0951 31.5825 -306.7295 -134.6138 > 172.1157 > 12 15 964 964.0 4th-Ventricle -212.5151 112.4167 -288.3225 0. > 288.3225 > 13 16 18186 18186.0 Brain-Stem -234.2281 112.8928 -319.7348 0. > 319.7348 > 14 17 4114 4114.0 Left-Hippocampus -261.7396 17.4063 -339.8024 > -223.4028 116.3996 > 15 18 1513 1513.0 Left-Amygdala -253.4237 8.8525 -288.2225 -232.8777 > 55.3447 > 16 24 847 847.0 CSF -257.5531 13.5256 -300.9257 -212.2279 88.6977 > 17 26 535 535.0 Left-Accumbens-area -227.1246 45.3633 -360.7124 > -138.9498 221.7626 > 18 28 3786 3786.0 Left-VentralDC -270.4991 24.1379 -308.4358 -148.3388 > 160.0970 > 19 30 35 35.0 Left-vessel -239.3001 10.2992 -259.7188 -227.2777 32.4411 > 20 31 1442 1442.0 Left-choroid-plexus -230.4919 15.5479 -280.8550 > -169.9589 110.8961 > 21 41 223786 223786.0 Right-Cerebral-White-Matter -226.0802 45.5920 > -388.7630 99.2566 488.0197 > 22 43 4499 4499.0 Right-Lateral-Ventricle -218.3645 29.3800 -283.5730 > -136.7349 146.8381 > 23 44 124 124.0 Right-Inf-Lat-Vent -224.9
[Freesurfer] Aparc stats with different input
Hi, I have a PET volume that is registered to a recon, then projected to the surface via vol2surf. I would like to pull stats for the PET using aparc regions. Should I use mri_annotation2label, then pull stats for each label? Or is there something similar to mri_segstats, ie. --annot lh.aparc.annot --in pet_surf.mgz --ctab-default --sum stats.table ? Thank you for your help! Sara ___ 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] Aparc stats with different input
I would use mri_vol2vol to map the PET into the anatomical space, then use mri_segstats to compute the statistics. doug On 10/22/2014 02:50 PM, Makaretz, Sara Johanna wrote: > Hi, > I have a PET volume that is registered to a recon, then projected to the > surface via vol2surf. I would like to pull stats for the PET using aparc > regions. Should I use mri_annotation2label, then pull stats for each label? > Or is there something similar to mri_segstats, ie. --annot lh.aparc.annot > --in pet_surf.mgz --ctab-default --sum stats.table ? > Thank you for your help! > Sara > ___ > 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] Creating an ROI mask for Cortical Thickness Analysis
Hello Freesurfer’s I am trying to look at the cortical thickness for a specific ROI on the cortical surface (Primary Auditory Cortex: transverse temporal gyri). I found a specific tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) however the tutorial assumes I already have an ROI mask created. I was wondering if anyone had any tips on creating an ROI for the cortical surface from the parcellation/annotation files. I know you can “hand-draw” ROI’s in tkmedit or freeview but I would prefer something less subjective that doesn’t rely on my untrained eye and unsteady hand! Thanks in advance. Best, Michael S. ___ 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] Parenchyma over CSF ratio
Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ? Thank you, Mahmoud ___ 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] Creating an ROI mask for Cortical Thickness Analysis
Why not just get it from the ?h.aparc.stats file? On 10/22/2014 03:43 PM, Smith, Michael wrote: > Hello Freesurfer’s > > I am trying to look at the cortical thickness for a specific ROI on > the cortical surface (Primary Auditory Cortex: transverse temporal > gyri). I found a specific tutorial > (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) > however the tutorial assumes I already have an ROI mask created. I was > wondering if anyone had any tips on creating an ROI for the cortical > surface from the parcellation/annotation files. I know you can > “hand-draw” ROI’s in tkmedit or freeview but I would prefer something > less subjective that doesn’t rely on my untrained eye and unsteady > hand! Thanks in advance. > > Best, > > Michael S. > > > > ___ > 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] Sulcal CSF Volume
Hello FreeSurfer Experts, Is it possible to estimate the sulcal CSF volume in Freesurfer processing? If not directly are there any indirect means that can give me an estimate? Thank you Mohammed Goryawala, PhD Department of Radiology Miller School of Medicine, University of Miami ___ 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 trouble with FTLD subjects
Hi All, I'm running a number of subjects who have FTLD and their surfarce/parcellation outputs are quite poor (especially in the frontal lobe obviously). Are there any expert commands that can be used to attempt to fix this issue without having to do individual edits? Most of the subjects have underestimations in most frontal gyri and insula. Thanks a lot, Adam Adam Mezher USC Imaging Genetics Center Marina Del Rey, CA ___ 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] freesurfer trouble with FTLD subjects
Hi Adam it's impossible to say without seeing some examples. If you upload a problematic subject (the entire subject directory from recon-all) we will take a look cheers Bruce On Wed, 22 Oct 2014, Adam Mezher wrote: > Hi All, > I'm running a number of subjects who have FTLD and their > surfarce/parcellation outputs are quite poor (especially in the frontal lobe > obviously). Are there any expert commands that can be used to attempt to fix > this issue without having to do individual edits? Most of the subjects have > underestimations in most frontal gyri and insula. > > Thanks a lot, > Adam > > Adam Mezher > USC Imaging Genetics Center > Marina Del Rey, CA > > ___ 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] longitudinal base template creation with one timepoint
Dear FreeSurfer Experts, I am interested in how the longitudinal stream creates a base template with only a single image. Could someone please explain how or point me to a reference as to how this is accomplished? Thank you, Tracy Melzer ___ 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] longitudinal base template creation with one timepoint
Hi Tracy, When you call recon-all -base simply pass only the single time point -tp. Best Martin Sent via my smartphone, please excuse brevity. Original message From: Tracy Melzer Date:10/22/2014 10:59 PM (GMT-05:00) To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] longitudinal base template creation with one timepoint Dear FreeSurfer Experts, I am interested in how the longitudinal stream creates a base template with only a single image. Could someone please explain how or point me to a reference as to how this is accomplished? Thank you, Tracy Melzer ___ 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] longitudinal base template creation with one timepoint
Hi Tracy, You can check out this page , on our FreeSurferWiki to find out more information on longitudinal processing: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing Also, our database of publications related to FreeSurfer in general is here: https://www.zotero.org/freesurfer Best, Lee From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Tracy Melzer Sent: Wednesday, October 22, 2014 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] longitudinal base template creation with one timepoint Dear FreeSurfer Experts, I am interested in how the longitudinal stream creates a base template with only a single image. Could someone please explain how or point me to a reference as to how this is accomplished? Thank you, Tracy Melzer ___ 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.
