Re: [Freesurfer] interpreting file (cache.th13.abs.y.ocn.dat) from longitudinal vertex-wise analysis
External Email - Use Caution Thanks for the info, Dr. Greve! So for the files I used for the --y argument were stacked files of this file: lh.long.thickness-spc.fwhm10.fsaverage.mgh or rh.long.thickness-spc.fwhm10.fsaverage.mgh. So would my interpretation of the ocn.dat file be that each value is the symmetrized percent change in thickness of the significant cluster for each subject? Thanks again, Batool ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] interpreting file (cache.th13.abs.y.ocn.dat) from longitudinal vertex-wise analysis
External Email - Use Caution Hi FreeSurfer team, After running longitudinal FS, and running mri_glmfit using files that measured spc, we found clusters associated with our continuous variable (WMH volume) after controlling for other covariates. I was wondering though, do the values found in cache.th13.abs.y.ocn.dat reflect the change in thickness (as measured by spc) for each subject of the cluster found to be significantly associated? I read other posts that it was a value of thickness of each cluster, but I wasn't sure if the same was true for a longitudinal analysis (spc), as the file contains both positive and negative numbers. Thanks so much for your help! Batool ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] extracting beta coefficients and p-values
External Email - Use Caution Thanks Dr. Greve, I'll CC the FS support team this time as well. That's correct, I got the contrasts.sig.mgh file from QDEC. So in order to get the p-values of each of the associations (for ex: age and cortical thinning), which command and input file should I use? Would it still be the mri_segstats command, but without the --avgwf option? Thanks again for your help and time! Batool From: Douglas N. Greve Sent: Monday, August 24, 2020 10:11 AM To: Rizvi, Batool ; Freesurfer support list Subject: Re: [Freesurfer] extracting beta coefficients and p-values answers below. also, please remember to post to the list On 8/21/2020 6:52 PM, Rizvi, Batool wrote: External Email - Use Caution Thank you Dr. Greve! This is very helpful! Just to confirm, similar to taking the effect of age, if I wanted to get the beta of Parietal WMH (my main continuous IV), I would just average betas 5-8? I forgot to add this in my previous email, but I'm also trying to extract p-values of all the variables involved, and wasn't sure how to. I tried running a couple different commands. When I ran this below command, I got a file with 1 column of 8 numbers: mri_segstats --i contrasts.sig.mgh --annot fsaverage lh lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot --excludeid 0 --avgwf avgwfsig.dat where did contrasts.sig.mgh come from? Was this created by QDEC? But when I tried the below command, I got a file with 1 number. mri_segstats --i lh-Avg-long.thickness-spc-Parietal_WMH-Cor/sig.mgh --annot fsaverage lh lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot --excludeid 0 --avgwf avgwfsig2.dat >From the 1st way (using contrasts.sig.mgh): -0.27711 -2.51072 0.42697 0.62922 -0.85069 0.52623 1.00393 -0.42921 >From the 2nd way (using sig.mgh) -2.51072 I'm pasting my fsgd format once more: GroupDescriptorFile 1 Title ParietalWMH_age_gender_APOe_EC_left MeasurementName long.thickness-spc Class APOE_statusNO-genderF Class APOE_statusYES-genderF Class APOE_statusNO-genderM Class APOE_statusYES-genderM Variables Parietal_WMH age_years Avg_ECthickness Input W38284_base APOE_statusNO-genderF 0.732010 85.83 3.125000 .. (only listing the 1st Input line here) My contrast file (C.dat) looks like below: 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 And I'm trying to find p-values for these variables' associations w/ thickness: APOE status, gender, Parietal WMH, Age, Avg EC thickness. Each contrast will have a sig file. But the command above will compute the average significance, which really does not mean anything Thanks so much again for all the help! Batool 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] extracting beta coefficients and p-values
External Email - Use Caution Dear FreeSurfer experts, After running the longitudinal pipeline with QDEC, I needed beta-values of the associations between my main continuous variable and the significant cortical cluster, as well as of all the nuisance factors/categorical variables. Since the summary file doesn't list beta values, I attempted running this command to find beta coefficients: mri_segstats --i beta.mgh --annot fsaverage lh lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot --excludeid 0 --avgwf avgwf.dat >From this, I got this output file listing beta values for 1 cluster >(entorhinal cortex) that was related to my main continuous IV (parietal WMH). >I'm struggling to understand how to still compute 1 beta-coefficient per >variable from this list. I understand that this list, based on my fsgd file, >can be split into 4 sets of numbers, but I'm not sure what do next. avgwf.dat: 0.93879 -8.80748 0.38452 3.13252 -0.09493 -0.13107 -0.09960 -0.31087 -0.02291 0.03127 -0.02417 -0.07858 0.13087 1.80749 0.32535 0.64947 Below is how my fsgd file was structured: GroupDescriptorFile 1 Title ParietalWMH_age_gender_APOe_EC_left MeasurementName long.thickness-spc Class APOE_statusNO-genderF Class APOE_statusYES-genderF Class APOE_statusNO-genderM Class APOE_statusYES-genderM Variables Parietal_WMH age_years Avg_ECthickness Input W38284_base APOE_statusNO-genderF 0.732010 85.83 3.125000 .. (only listing the 1st Input line here) My contrast file (C.dat) looks like below: 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 So basically, I would like to get beta coefficients for the below variables: * Parietal WMH * Age * Gender * APOE status * Average EC thickness (baseline values) Thank you so much in advance for your help! Batool ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] QDEC and comparing two conditions
Hi - I'm still wondering what would be the best method to perform the mentioned steps. Additionally, would mri_compute_overlap provide output related to spatial overlap and difference, that we're looking for? Is it possible to do this with thickness, or maybe not - because it doesn't consider area? Just wondering, as we only performed QDEC using thickness so far. Thanks so much, Batool From: Rizvi, Batool Sent: Tuesday, November 28, 2017 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: QDEC and comparing two conditions Hi FreeSurfer experts, We calculated the correlation between thickness two different behavioral conditions using QDEC. We now want to compare the spatial overlap and difference in thickness-correlation between the two behavioral conditions. We would like to do this both visually as well as statistically. Is there an option to do this either in QDEC or in the command line? Thanks for your time! Batool ___ 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] QDEC and comparing two conditions
Hi FreeSurfer experts, We calculated the correlation between thickness two different behavioral conditions using QDEC. We now want to compare the spatial overlap and difference in thickness-correlation between the two behavioral conditions. We would like to do this both visually as well as statistically. Is there an option to do this either in QDEC or in the command line? Thanks for your time! Batool ___ 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] TRACULA - error
Hi, I'm running tracula using the following command: (Note: I'm replacing actual paths with made up paths) trac-all -prep -c /path/to/my/config.sh And for some reason it stops running while working on the first subject (creates the folder for the first subject), with this error: if: Expression Syntax. It doesn't show any errors before this line. The line before this one was copying over the bvecs file to the new path (cp /path/to/my/bvecs.txt path/to/dmri/dwi_orig.bvecs) Is there something I'm doing wrong? Thanks, Batool ___ 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 - subjects with different number of directions
Thanks Dr. Yendiki, that was my gut feeling as well. Thanks for the info! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu] Sent: Wednesday, March 29, 2017 10:55 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions You are trying to combine data from two very different protocols. This is not advisable. I would exclude those 5 subjects. From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Rizvi, Batool" <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, March 29, 2017 at 10:43 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions So sorry - one last question. Would it be also ok if the value of the bval numbers are also different? One set of subjects/bvals have 15 numbers with the value of 800, while the 5 of them have the 48 numbers with value of 1000. Is this an issue as well? Thanks Dr. Yendiki, for all the help! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>] Sent: Wednesday, March 29, 2017 9:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions You should use the same 16 gradient directions as the ones that your 16-direction scans have. You have to look at the gradient tables from subjects with each type of scan. Once you have identified which volumes in the 49-volume series were acquired with those 16 directions, you can use something like: mri_convert --i input_dwis --f 0 5 17 --o output_dwis where you'd replace my "0 5 17" with your list of the (0-based) numbers of the volumes that you want to extract (16 numbers in your case). From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>] Sent: Wednesday, March 29, 2017 9:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions Thank you. That makes sense, and in that case we'll only use 16 directions for all subjects, including in those 5. Just wondering if you had any pointers on which software could be used to extract the 16 directions from the 49, or if it's ususally done by code in matlab? Also, in terms of choosing the 16 directions to pull out from these 5 files, would you use the first 16 directions in the file, or the most evenly distributed 16 directions? Thanks again! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>] Sent: Wednesday, March 29, 2017 8:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions Hi Batool - Yes, it would be a problem. It'd be similar to having some scans with one spatial resolution and some with another, or administering one questionnaire to some of your subjects and a different one to the others and then trying to compare the answers. If the 16 directions are a subset of the 49 directions, then you can discard the remaining 33 directions from the subjects that have 49. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>] Sent: Wednesday, March 29, 2017 8:37 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA - subjects with different number of directions Hi, We were wondering if it would be an issue if we used a dataset in which we included 5 subjects that have a different number of directions (49 directions) than the rest of the subjects with a standard number (16 dire
Re: [Freesurfer] TRACULA - subjects with different number of directions
So sorry - one last question. Would it be also ok if the value of the bval numbers are also different? One set of subjects/bvals have 15 numbers with the value of 800, while the 5 of them have the 48 numbers with value of 1000. Is this an issue as well? Thanks Dr. Yendiki, for all the help! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu] Sent: Wednesday, March 29, 2017 9:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions You should use the same 16 gradient directions as the ones that your 16-direction scans have. You have to look at the gradient tables from subjects with each type of scan. Once you have identified which volumes in the 49-volume series were acquired with those 16 directions, you can use something like: mri_convert --i input_dwis --f 0 5 17 --o output_dwis where you'd replace my "0 5 17" with your list of the (0-based) numbers of the volumes that you want to extract (16 numbers in your case). From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu] Sent: Wednesday, March 29, 2017 9:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions Thank you. That makes sense, and in that case we'll only use 16 directions for all subjects, including in those 5. Just wondering if you had any pointers on which software could be used to extract the 16 directions from the 49, or if it's ususally done by code in matlab? Also, in terms of choosing the 16 directions to pull out from these 5 files, would you use the first 16 directions in the file, or the most evenly distributed 16 directions? Thanks again! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu] Sent: Wednesday, March 29, 2017 8:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions Hi Batool - Yes, it would be a problem. It'd be similar to having some scans with one spatial resolution and some with another, or administering one questionnaire to some of your subjects and a different one to the others and then trying to compare the answers. If the 16 directions are a subset of the 49 directions, then you can discard the remaining 33 directions from the subjects that have 49. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu] Sent: Wednesday, March 29, 2017 8:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA - subjects with different number of directions Hi, We were wondering if it would be an issue if we used a dataset in which we included 5 subjects that have a different number of directions (49 directions) than the rest of the subjects with a standard number (16 directions). Even if the preprocessing steps work, will it be an issue comparing the subjects statistically? If so, how can we treat the 5 subjects differently, but still include them in our study? Thank you! Batool ___ 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 - subjects with different number of directions
Thank you. That makes sense, and in that case we'll only use 16 directions for all subjects, including in those 5. Just wondering if you had any pointers on which software could be used to extract the 16 directions from the 49, or if it's ususally done by code in matlab? Also, in terms of choosing the 16 directions to pull out from these 5 files, would you use the first 16 directions in the file, or the most evenly distributed 16 directions? Thanks again! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu] Sent: Wednesday, March 29, 2017 8:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions Hi Batool - Yes, it would be a problem. It'd be similar to having some scans with one spatial resolution and some with another, or administering one questionnaire to some of your subjects and a different one to the others and then trying to compare the answers. If the 16 directions are a subset of the 49 directions, then you can discard the remaining 33 directions from the subjects that have 49. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu] Sent: Wednesday, March 29, 2017 8:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA - subjects with different number of directions Hi, We were wondering if it would be an issue if we used a dataset in which we included 5 subjects that have a different number of directions (49 directions) than the rest of the subjects with a standard number (16 directions). Even if the preprocessing steps work, will it be an issue comparing the subjects statistically? If so, how can we treat the 5 subjects differently, but still include them in our study? Thank you! Batool ___ 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] TRACULA - subjects with different number of directions
Hi, We were wondering if it would be an issue if we used a dataset in which we included 5 subjects that have a different number of directions (49 directions) than the rest of the subjects with a standard number (16 directions). Even if the preprocessing steps work, will it be an issue comparing the subjects statistically? If so, how can we treat the 5 subjects differently, but still include them in our study? Thank you! Batool ___ 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] hippocampal subfields - T1
Got it, thanks for the help! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: Thursday, February 23, 2017 4:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields - T1 Hi Batool, It’s not ideal, but if FreeSurfer does a decent job with the recon, something decent should come out of the subfields. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 23 Feb 2017, at 20:11, Rizvi, Batool <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote: Hi, I was wondering if the hippocampal subfields analysis can still run on a lower resolution T1 scan than 1mm? One of our datasets has T1 scans with these dimensions: .93 x .93 x 1.3 . Would it still run on this dataset, if it's not the standard 1mm to begin with? Thanks! Batool ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] hippocampal subfields - T1
Hi, I was wondering if the hippocampal subfields analysis can still run on a lower resolution T1 scan than 1mm? One of our datasets has T1 scans with these dimensions: .93 x .93 x 1.3 . Would it still run on this dataset, if it's not the standard 1mm to begin with? Thanks! Batool ___ 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] hippocampal subfields analysis command
Hi Eugenio, Here are my outputs: ls e009723_FS (one of my subject's freesurfer folder): bem FS1.sh FS2.sh FS4.sh label mri scripts src stats surf tmp touch trash - you can ignore the FS#.sh files - these are matlab script files we run. ls mri/lh.hippoSfVolumes*.txt: mri/lh.hippoSfVolumes-T1.v10.txt Thanks! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: Monday, February 13, 2017 1:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields analysis command That’s weird. What is the output of the following command? ls /path/to/my/subjects/freesurferfolder And of this one: ls /path/to/my/subjects/freesurferfolder/SUBJECT/mri/lh.hippoSfVolumes*.txt (where SUBJECT is a subject of your choice) Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13 Feb 2017, at 17:04, Rizvi, Batool <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote: Hi Eugenio, That's actually the issue, it doesn't generate any file at all.. there's no hippo.txt in the folder where I run it, or in the subject's directory that I had specified. Batool From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>] Sent: Monday, February 13, 2017 11:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields analysis command Hi Batool What are the contents of hippo.txt? Just empty? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com<http://www.jeiglesias.com/> http://cmictig.cs.ucl.ac.uk/ On 13 Feb 2017, at 16:41, Rizvi, Batool <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote: Hi, I'm having trouble getting any output from the hippocampal subfield analysis command. I entered in: quantifyHippocampalSubfields.sh T1 hippo.txt /path/to/my/subjects/freesurferfolder I tried both ways of having the environmental variable subjects directory defined to the freesurfer folder of the subjects (used *'s here for subjects and their freesurfer folder), but it still gives no output. It just says: Gathering results from subjects in: /path/to/my/subjects/freesurferfolder Using the suffix name: T1 And writing them to: hippo.txt What am I doing wrong here? Thanks so much! Batool ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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] hippocampal subfields analysis command
Hi Eugenio, That's actually the issue, it doesn't generate any file at all.. there's no hippo.txt in the folder where I run it, or in the subject's directory that I had specified. Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: Monday, February 13, 2017 11:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields analysis command Hi Batool What are the contents of hippo.txt? Just empty? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13 Feb 2017, at 16:41, Rizvi, Batool <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote: Hi, I'm having trouble getting any output from the hippocampal subfield analysis command. I entered in: quantifyHippocampalSubfields.sh T1 hippo.txt /path/to/my/subjects/freesurferfolder I tried both ways of having the environmental variable subjects directory defined to the freesurfer folder of the subjects (used *'s here for subjects and their freesurfer folder), but it still gives no output. It just says: Gathering results from subjects in: /path/to/my/subjects/freesurferfolder Using the suffix name: T1 And writing them to: hippo.txt What am I doing wrong here? Thanks so much! Batool ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] hippocampal subfields analysis command
Hi, I'm having trouble getting any output from the hippocampal subfield analysis command. I entered in: quantifyHippocampalSubfields.sh T1 hippo.txt /path/to/my/subjects/freesurferfolder I tried both ways of having the environmental variable subjects directory defined to the freesurfer folder of the subjects (used *'s here for subjects and their freesurfer folder), but it still gives no output. It just says: Gathering results from subjects in: /path/to/my/subjects/freesurferfolder Using the suffix name: T1 And writing them to: hippo.txt What am I doing wrong here? Thanks so much! Batool ___ 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 6.0 with some of the analyses
Thanks for your responses! Sorry for the naive question, but I'm wondering which commands I'd use to re-process all the data from 5.3. Can I run recon-all -all, and it will go through all the steps that it would if I ran it from the start? Or would it skip certain steps if it finds certain files existing already. I'm pretty sure the former is true, but just wanted to confirm. Thanks again! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: Thursday, January 26, 2017 11:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses Dear Batool, Sorry for missing your message. And dear Adam: Thanks for covering me! That’s exactly my standard answer to that question ;-) Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 26 Jan 2017, at 15:55, Adam Martersteck <acmar...@gmail.com<mailto:acmar...@gmail.com>> wrote: I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to reproduce" e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer to achieve comparable results with your study. I think the general consensus is "how many subjects do you have?" -- if it's less than 50, you may want to just rerun v6 on your subjects as it should preserve the edits -- but it's recommended you still open them up and double check. -Adam On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote: Hi, Can anyone comment on my question below? I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0. Thanks so much! Batool ________ From: Rizvi, Batool Sent: Wednesday, January 25, 2017 12:54 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: freesurfer 6.0 with some of the analyses Hi, I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us starting over for the analyses we've already done in 5.3 for that study? Thank you! Batool ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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] freesurfer 6.0 with some of the analyses
Hi, Can anyone comment on my question below? I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0. Thanks so much! Batool From: Rizvi, Batool Sent: Wednesday, January 25, 2017 12:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: freesurfer 6.0 with some of the analyses Hi, I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us starting over for the analyses we've already done in 5.3 for that study? Thank you! Batool ___ 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 6.0 with some of the analyses
Hi, I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us starting over for the analyses we've already done in 5.3 for that study? Thank you! Batool ___ 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] incorrect pial surfaces after watershed adjustment
Hi Bruce, Running -autorecon2 -autorecon3 did not seem to fix the surfaces for this subject. Do you have any further suggestions on what we could try to correct the surfaces? Thank you! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu] Sent: Wednesday, December 14, 2016 1:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment Ohkay thanks, we'll go ahead and run autorecon2 and autorecon 3 on this subject then. Thanks! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, December 14, 2016 1:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment Hi Batool if you need to change the watershed you will need to rerun everything from there forward. All of autorecon2 and autorecon3 I think at least cheers Bruce On Wed, 14 Dec 2016, Rizvi, Batool wrote: > > Hi FreeSurfer experts, > > > > We have a subject on which we had to do adjust the watershed parameters for, > since there was some > brain missing from the brainmask.mgz. The watershed itself worked, but after > that, we needed to > regenerate the surfaces after the bad skull strip was fixed, and we ran > "recon-all -autorecon-pial > -subjid " > > > > That seemed to not work though, and it still shows that the surfaces do not > include the new brain > matter. Attached is an image of the output. Is there anything else we can try > to regenerate these > surfaces correctly? > > > > Thank you! > > Batool > > > ___ 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
Re: [Freesurfer] incorrect pial surfaces after watershed adjustment
Ohkay thanks, we'll go ahead and run autorecon2 and autorecon 3 on this subject then. Thanks! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, December 14, 2016 1:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment Hi Batool if you need to change the watershed you will need to rerun everything from there forward. All of autorecon2 and autorecon3 I think at least cheers Bruce On Wed, 14 Dec 2016, Rizvi, Batool wrote: > > Hi FreeSurfer experts, > > > > We have a subject on which we had to do adjust the watershed parameters for, > since there was some > brain missing from the brainmask.mgz. The watershed itself worked, but after > that, we needed to > regenerate the surfaces after the bad skull strip was fixed, and we ran > "recon-all -autorecon-pial > -subjid " > > > > That seemed to not work though, and it still shows that the surfaces do not > include the new brain > matter. Attached is an image of the output. Is there anything else we can try > to regenerate these > surfaces correctly? > > > > Thank you! > > Batool > > > ___ 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] white matter segmentation incorrect after intensity change
Hi Bruce, I noticed I did it incorrectly, so I started running an hour ago just recon-all -autorecon2-cp -autorecon2 without the -all, about an hour ago. It's starting to generate output now, not sure why it didn't at all last time (may have to do with our new cluster). Will let you know if anything goes wrong with the output this time.. Thanks! Batool From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, December 12, 2016 11:34 AM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change Hi Batool you don't need -all and -autorecon2-cp -aurorecon3 (-all is both of those and more). It must have generated some output. Is there a recon-all.log in the freesurferfolder/scripts dir? cheers Bruce On Mon, 12 Dec 2016, Rizvi, Batool wrote: > > Hi Bruce, > We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3 > -subjid freesurferfolder. > We got no output files from that, but I'm wondering if freesurfer didn't run > only because we incorrectly ran this command with the '-all', or do you think > there was some other reason? We ran this on the cluster, and it generated no > error logs. > > Thanks again for your help! > > Batool___ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, December 01, 2016 5:21 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity > change > > sure, good luck > Bruce > On Thu, 1 Dec 2016, Rizvi, Batool wrote: > >> Sounds great, thanks again for your help and will try out your >> recommendations. >> Have a great day! >> >> B >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, December 01, 2016 4:27 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] white matter segmentation incorrect after >> intensity change >> >> yes, you can remove the control.dat file and run autorecon2-cp and >> autorecon3. Should only take a couple of hours depending on your >> processor >> On Thu, 1 Dec 2016, Rizvi, Batool wrote: >> >>> >>> Hi Bruce, >>> Thanks so much for the feedback, that is very helpful. We'll try deleting >>> the control points then. Is there a quick way to rerun recon-all without >>> having it take up to 5-8 hours? >>> >>> Also, a separate question, when running autorecon, after edits to the white >>> matter and pial surfaces, should we run the command -autorecon2 >>> -autorecon3, or would that include too many steps? I read that it's >>> recommended to run from -autorecon2-cp instead? >>> >>> >>> Thanks so much for your help, >>> B >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, December 01, 2016 4:04 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] white matter segmentation incorrect after >>> intensity change >>> >>> the problme is that you have several control points in voxels that aren't >>> entirely wm. For example, 129, 134, 173 is a control point and it has no wm >>> in it. This causes the intensity in that region to go up way too high, as >>> we will normalize the control points to the desired wm intensity (110). I >>> ran it without any control points and it worked pretty well. You should >>> probably get rid of your control.dat. If you think that those thin frontal >>> strands should go out a bit further, since some voxels that are entirely >>> white matter (e.g. 134, 135, 162) but have an intensity that is less than >>> 110 (this one is 103 after normalizating) and it will bring the intensity >>> up a bit in that entire region (by the ratio of 110/103). >>> >>> On Thu, 1 Dec 2016, Rizvi, Batool wrote: >>> >>>> Hi Bruce, >>>> Thanks for your reply. It is actually brighter on the brainmask.mgz than >>>> the orig.mgz when I checked. I'm uploading the freesurfer subject here. >>>> >>>> Thanks! >>>
Re: [Freesurfer] white matter segmentation incorrect after intensity change
Hi Bruce, We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3 -subjid freesurferfolder. We got no output files from that, but I'm wondering if freesurfer didn't run only because we incorrectly ran this command with the '-all', or do you think there was some other reason? We ran this on the cluster, and it generated no error logs. Thanks again for your help! Batool___ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 5:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change sure, good luck Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote: > Sounds great, thanks again for your help and will try out your > recommendations. > Have a great day! > > B > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, December 01, 2016 4:27 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity > change > > yes, you can remove the control.dat file and run autorecon2-cp and > autorecon3. Should only take a couple of hours depending on your > processor > On Thu, 1 Dec 2016, Rizvi, Batool wrote: > >> >> Hi Bruce, >> Thanks so much for the feedback, that is very helpful. We'll try deleting >> the control points then. Is there a quick way to rerun recon-all without >> having it take up to 5-8 hours? >> >> Also, a separate question, when running autorecon, after edits to the white >> matter and pial surfaces, should we run the command -autorecon2 -autorecon3, >> or would that include too many steps? I read that it's recommended to run >> from -autorecon2-cp instead? >> >> >> Thanks so much for your help, >> B >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, December 01, 2016 4:04 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] white matter segmentation incorrect after >> intensity change >> >> the problme is that you have several control points in voxels that aren't >> entirely wm. For example, 129, 134, 173 is a control point and it has no wm >> in it. This causes the intensity in that region to go up way too high, as >> we will normalize the control points to the desired wm intensity (110). I >> ran it without any control points and it worked pretty well. You should >> probably get rid of your control.dat. If you think that those thin frontal >> strands should go out a bit further, since some voxels that are entirely >> white matter (e.g. 134, 135, 162) but have an intensity that is less than >> 110 (this one is 103 after normalizating) and it will bring the intensity >> up a bit in that entire region (by the ratio of 110/103). >> >> On Thu, 1 Dec 2016, Rizvi, Batool wrote: >> >>> Hi Bruce, >>> Thanks for your reply. It is actually brighter on the brainmask.mgz than >>> the orig.mgz when I checked. I'm uploading the freesurfer subject here. >>> >>> Thanks! >>> BR >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, December 01, 2016 2:31 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] white matter segmentation incorrect after >>> intensity change >>> >>> hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not >>> really possible to diagnose from a single slice from a single subject. If >>> you tar, gzip and upload the subject one of us will take a look >>> >>> cheers >>> Bruce >>> On Thu, 1 >>> Dec 2016, Rizvi, Batool wrote: >>> >>>> >>>> Hi FreeSurfer experts, >>>> >>>> >>>> >>>> After running -autorecon2 and -autorecon3, we're seeing issues for some of >>>> the subjects, which now start showing changes in intensity/brightness in >>>> some voxels, and this increased intensity is now missed by the white matter >>>> and grey matter segmentation, and is labeled as no
[Freesurfer] poor segmentation and skull-strip = due to talairach?
Hi FreeSurfer team, We have a couple of subjects that have really poor segmentation and skull-strip as well, that seem beyond fixing with just control points or WM edits. I'm wondering if this occurred because of earlier in the stream, there was a bad talairach transform? I went back to see the talairach, and it also looked irreparable. So this time, I tried using the other method of producing a talairach transform (mritotal), but this only made it much worse than before. How can I regenerate the talairach so that it will at least cleanly fit the lines of at least the target volume? Thanks very much! Batool ___ 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] white matter segmentation incorrect after intensity change
Sounds great, thanks again for your help and will try out your recommendations. Have a great day! B From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change yes, you can remove the control.dat file and run autorecon2-cp and autorecon3. Should only take a couple of hours depending on your processor On Thu, 1 Dec 2016, Rizvi, Batool wrote: > > Hi Bruce, > Thanks so much for the feedback, that is very helpful. We'll try deleting the > control points then. Is there a quick way to rerun recon-all without having > it take up to 5-8 hours? > > Also, a separate question, when running autorecon, after edits to the white > matter and pial surfaces, should we run the command -autorecon2 -autorecon3, > or would that include too many steps? I read that it's recommended to run > from -autorecon2-cp instead? > > > Thanks so much for your help, > B > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, December 01, 2016 4:04 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity > change > > the problme is that you have several control points in voxels that aren't > entirely wm. For example, 129, 134, 173 is a control point and it has no wm > in it. This causes the intensity in that region to go up way too high, as > we will normalize the control points to the desired wm intensity (110). I > ran it without any control points and it worked pretty well. You should > probably get rid of your control.dat. If you think that those thin frontal > strands should go out a bit further, since some voxels that are entirely > white matter (e.g. 134, 135, 162) but have an intensity that is less than > 110 (this one is 103 after normalizating) and it will bring the intensity > up a bit in that entire region (by the ratio of 110/103). > > On Thu, 1 Dec 2016, Rizvi, Batool wrote: > >> Hi Bruce, >> Thanks for your reply. It is actually brighter on the brainmask.mgz than the >> orig.mgz when I checked. I'm uploading the freesurfer subject here. >> >> Thanks! >> BR >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, December 01, 2016 2:31 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] white matter segmentation incorrect after >> intensity change >> >> hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not >> really possible to diagnose from a single slice from a single subject. If >> you tar, gzip and upload the subject one of us will take a look >> >> cheers >> Bruce >> On Thu, 1 >> Dec 2016, Rizvi, Batool wrote: >> >>> >>> Hi FreeSurfer experts, >>> >>> >>> >>> After running -autorecon2 and -autorecon3, we're seeing issues for some of >>> the subjects, which now start showing changes in intensity/brightness in >>> some voxels, and this increased intensity is now missed by the white matter >>> and grey matter segmentation, and is labeled as non-brain matter. >>> >>> >>> >>> Attached is an example of a subject's brain that was segmented incorrectly, >>> which we think is due to the intensity around that frontal region. We hadn't >>> added control points in that region, so we are unsure what the cause of the >>> intensity change is. In our first pass before running -autorecon2 >>> -autorecon3, we did not notice this error or the intensity values to be so >>> bright for that region. >>> >>> >>> >>> Thanks for your help! >>> >>> BR >>> >>> >>> > ___ > 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 wa
Re: [Freesurfer] white matter segmentation incorrect after intensity change
Hi Bruce, Thanks so much for the feedback, that is very helpful. We'll try deleting the control points then. Is there a quick way to rerun recon-all without having it take up to 5-8 hours? Also, a separate question, when running autorecon, after edits to the white matter and pial surfaces, should we run the command -autorecon2 -autorecon3, or would that include too many steps? I read that it's recommended to run from -autorecon2-cp instead? Thanks so much for your help, B From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 4:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change the problme is that you have several control points in voxels that aren't entirely wm. For example, 129, 134, 173 is a control point and it has no wm in it. This causes the intensity in that region to go up way too high, as we will normalize the control points to the desired wm intensity (110). I ran it without any control points and it worked pretty well. You should probably get rid of your control.dat. If you think that those thin frontal strands should go out a bit further, since some voxels that are entirely white matter (e.g. 134, 135, 162) but have an intensity that is less than 110 (this one is 103 after normalizating) and it will bring the intensity up a bit in that entire region (by the ratio of 110/103). On Thu, 1 Dec 2016, Rizvi, Batool wrote: > Hi Bruce, > Thanks for your reply. It is actually brighter on the brainmask.mgz than the > orig.mgz when I checked. I'm uploading the freesurfer subject here. > > Thanks! > BR > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, December 01, 2016 2:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity > change > > hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not > really possible to diagnose from a single slice from a single subject. If > you tar, gzip and upload the subject one of us will take a look > > cheers > Bruce > On Thu, 1 > Dec 2016, Rizvi, Batool wrote: > >> >> Hi FreeSurfer experts, >> >> >> >> After running -autorecon2 and -autorecon3, we're seeing issues for some of >> the subjects, which now start showing changes in intensity/brightness in >> some voxels, and this increased intensity is now missed by the white matter >> and grey matter segmentation, and is labeled as non-brain matter. >> >> >> >> Attached is an example of a subject's brain that was segmented incorrectly, >> which we think is due to the intensity around that frontal region. We hadn't >> added control points in that region, so we are unsure what the cause of the >> intensity change is. In our first pass before running -autorecon2 >> -autorecon3, we did not notice this error or the intensity values to be so >> bright for that region. >> >> >> >> Thanks for your help! >> >> BR >> >> >> ___ 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
Re: [Freesurfer] white matter segmentation incorrect after intensity change
Hi Bruce, Thanks for your reply. It is actually brighter on the brainmask.mgz than the orig.mgz when I checked. I'm uploading the freesurfer subject here. Thanks! BR From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, December 01, 2016 2:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity change hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look cheers Bruce On Thu, 1 Dec 2016, Rizvi, Batool wrote: > > Hi FreeSurfer experts, > > > > After running -autorecon2 and -autorecon3, we're seeing issues for some of > the subjects, which now start showing changes in intensity/brightness in > some voxels, and this increased intensity is now missed by the white matter > and grey matter segmentation, and is labeled as non-brain matter. > > > > Attached is an example of a subject's brain that was segmented incorrectly, > which we think is due to the intensity around that frontal region. We hadn't > added control points in that region, so we are unsure what the cause of the > intensity change is. In our first pass before running -autorecon2 > -autorecon3, we did not notice this error or the intensity values to be so > bright for that region. > > > > Thanks for your help! > > BR > > > FTLDES008_FS.tar Description: FTLDES008_FS.tar ___ 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.
