[Freesurfer] Two FS versions in different user accounts
Hi everyone, I'm sorry to bring this question up again, but I'm thinking to install version 5.1 in the same computer where version 5.0 is installed. However I'm thinking of installing the new one in another user account that I've created only for this porpuse. My question is, can I install and work in the new user independently? This way I won't need to be changing the subjects dir and the freesurfer environment each time I want to work with 5.0 or 5.1, right? Advice needed =) Thanks, Andreia ___ 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] Two FS versions in different user accounts
Hi Andreia yes, that should be fine. You really just need to change FREESURFER_HOME and the associated binary paths to use one version or the other. cheers Bruce On Fri, 27 Jan 2012, _andre...@sapo.pt wrote: Hi everyone, I'm sorry to bring this question up again, but I'm thinking to install version 5.1 in the same computer where version 5.0 is installed. However I'm thinking of installing the new one in another user account that I've created only for this porpuse. My question is, can I install and work in the new user independently? This way I won't need to be changing the subjects dir and the freesurfer environment each time I want to work with 5.0 or 5.1, right? Advice needed =) Thanks, Andreia ___ 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] control point guidance
Hi guys, We are currently trying to fix some errors in the white/pial surfaces where there are thin white matter strands by using control points, and are noticing a couple things: 1) The resulting WM surface in the area of the CPs can end up too far into the GM instead. Given that, is there any practical guidance for how to think about the surrounding spatial extent that is impacted by a given CP? i.e., How do CP's actually get used within mri_normalize in an algorithmic sense? 2) The surfaces are being impacted in places distant from the CPs. e.g., CP's placed in the left anterior temporal lobe are resulting in surface changes in the right anterior temporal lobe. And when I difference the original norm.mgz vs. the one obtained after using CP's, I'm seeing an odd pattern of intensity differences which is clearly not limited to just the area of the CP's (which would be my expectation). This is version 5.1. thanks, -MH -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave.Fax: 314-747-2182 St. Louis, MO 63110 Email: mha...@wustl.edu ___ 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] control point guidance
Hi Michael, I had the same problem too. It might be because of the type of scanner you are using. I added -washu_mprage flag, it pretty much helped me (I did not had to add a lot of controls points and so on so forth. You can go through the link below. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011695.html Hope it helps. -SK On Fri, Jan 27, 2012 at 12:06 PM, Michael Harms mha...@conte.wustl.eduwrote: Hi guys, We are currently trying to fix some errors in the white/pial surfaces where there are thin white matter strands by using control points, and are noticing a couple things: 1) The resulting WM surface in the area of the CPs can end up too far into the GM instead. Given that, is there any practical guidance for how to think about the surrounding spatial extent that is impacted by a given CP? i.e., How do CP's actually get used within mri_normalize in an algorithmic sense? 2) The surfaces are being impacted in places distant from the CPs. e.g., CP's placed in the left anterior temporal lobe are resulting in surface changes in the right anterior temporal lobe. And when I difference the original norm.mgz vs. the one obtained after using CP's, I'm seeing an odd pattern of intensity differences which is clearly not limited to just the area of the CP's (which would be my expectation). This is version 5.1. thanks, -MH -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave.Fax: 314-747-2182 St. Louis, MO 63110 Email: mha...@wustl.edu ___ 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 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] how can I view and process Freesurfer files using AFNI
Hello, I ran recon all on my subjects data which went well. Now I would like to use AFNI-SUMA to view it , how do I go about doing this. Thanks, Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. ___ 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] how can I view and process Freesurfer files using AFNI
Hello Rashmi, This is an AFNI issue. You'll have to read the SUMA manual and convert your Freesurfer files to AFNI-readable surfaces using @SUMA_Make_Spec_FS and other commands. There are too many steps to list here, but it is not too difficult once you get the hang of it. Anthony On 1/27/12 2:10 PM, Rashmi Singh wrote: Hello, I ran recon all on my subjects data which went well. Now I would like to use AFNI-SUMA to view it , how do I go about doing this. Thanks, Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. ___ 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. -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: ad...@fiu.edu Webpage: http://www.fiu.edu/~adick ___ 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] control point guidance
Hi Mike it's a bit hard to state the region of effect for the control points. Essentially we go through and label voxels as control points or not based on their intensity, intensity gradient and connectivity (that is, the must be 6-connected to other control points) then build a Voronoi diagram and each control point sets the scaling for its Voronoi triangle. Thus if you have a control point surrounded by others its region of effect is small, but one control point all by itself can have a large region of effect. Also, 5.1 applies the manually specified control points to the aseg normalization (norm.mgz), whereas older versions didn't. Not everyone is happy with this, so I think there is a backwards compatibility flag. Nick would know. Bruce On Fri, 27 Jan 2012, Sabin Khadka wrote: Hi Michael,I had the same problem too. It might be because of the type of scanner you are using. I added -washu_mprage flag, it pretty much helped me (I did not had to add a lot of controls points and so on so forth. You can go through the link below. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011695.html Hope it helps. -SK On Fri, Jan 27, 2012 at 12:06 PM, Michael Harms mha...@conte.wustl.edu wrote: Hi guys, We are currently trying to fix some errors in the white/pial surfaces where there are thin white matter strands by using control points, and are noticing a couple things: 1) The resulting WM surface in the area of the CPs can end up too far into the GM instead. Given that, is there any practical guidance for how to think about the surrounding spatial extent that is impacted by a given CP? i.e., How do CP's actually get used within mri_normalize in an algorithmic sense? 2) The surfaces are being impacted in places distant from the CPs. e.g., CP's placed in the left anterior temporal lobe are resulting in surface changes in the right anterior temporal lobe. And when I difference the original norm.mgz vs. the one obtained after using CP's, I'm seeing an odd pattern of intensity differences which is clearly not limited to just the area of the CP's (which would be my expectation). This is version 5.1. thanks, -MH -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mha...@wustl.edu ___ 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 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] Too many levels of symbolic links
usually that means a symbolic link is recursive or self-referential in some way. What does ls -l /Applications/freesurfer/subjects/fsaverage return? Bruce On Fri, 27 Jan 2012, cloud.c...@me.com wrote: I have subjects exiting with errors and I'm not sure why. The best clue I have is a line indicating Too many levels of symbolic links and an inability to read lh.BA1.label. Here are the last few lines of output: SUBJECTS_DIR/Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Too many levels of symbolic links ERROR reading /Applications/freesurfer/subjects/fsaverage/label/lh.BA1.label Darwin stat-240-26.sdsu.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s GB exited with ERRORS at Thu Jan 26 00:29:32 PST 2012 Can anyone tell me what is happening here? ___ 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.
Re: [Freesurfer] Verifying ICV in FS5
bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.que...@gmail.com wrote: Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2 program and I think I see some poor transformations. I've never really used it before though. Am I just looking at whether or not the green line lines up with the target image wm? Can you look at my pictures real quick? 040002_S04_test is from fs4 that is having problems. 040002_S04 is from fs3 and has a good icv value. Some of the blank spots are from my graphics drivers and unrelated to fs. tkregister2 also said the determinant of 040002_S04_test was 1.49544. Martin, Thank you for the idea. I did this, and got a much better icv. On fs3, where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. Using your idea on fs4, it was 1,819,485. Thank you so much to everyone for your help! Jeff On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec martin.ka...@gmail.com mailto:martin.ka...@gmail.com wrote: Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I then compare each ICV normalized aseg volume against an age matched group and only if the old-etiv-only ICV gives better estimates I use it. Cheers, Martin On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overall. # subjectname 090167_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1639959, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1639959.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1289194.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1299686, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1299686.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105595.114652, mm^3 # subjectname 090182_S01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1599981, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1599981.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1199694.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1205382, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1205382.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1114008.197334, mm^3 # subjectname 090187_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1826694, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1826694.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1381871.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1388801, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1388801.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume,
Re: [Freesurfer] Verifying ICV in FS5
Hi Jeff, I am not sure about which atlas, but concerning the transforms: 4.2 and earlier: talairach_with_skull.lta later versions: talairach.xfm I am pretty convinced that the way to check as described here http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk is correct in newer FS versions, but maybe double check with Nick. Best, Martin On Fri, 2012-01-27 at 13:39 -1000, Jeff Sadino wrote: bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.que...@gmail.com wrote: Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2 program and I think I see some poor transformations. I've never really used it before though. Am I just looking at whether or not the green line lines up with the target image wm? Can you look at my pictures real quick? 040002_S04_test is from fs4 that is having problems. 040002_S04 is from fs3 and has a good icv value. Some of the blank spots are from my graphics drivers and unrelated to fs. tkregister2 also said the determinant of 040002_S04_test was 1.49544. Martin, Thank you for the idea. I did this, and got a much better icv. On fs3, where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. Using your idea on fs4, it was 1,819,485. Thank you so much to everyone for your help! Jeff On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec martin.ka...@gmail.com mailto:martin.ka...@gmail.com wrote: Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I then compare each ICV normalized aseg volume against an age matched group and only if the old-etiv-only ICV gives better estimates I use it. Cheers, Martin On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overall. # subjectname 090167_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1639959, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1639959.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1289194.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1299686, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1299686.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105595.114652, mm^3 # subjectname 090182_S01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1599981, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1599981.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1199694.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1205382, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume,
